Compositions and methods for treating cep290-associated disease

ABSTRACT

Compositions and methods for treatment of CEP290 related diseases are disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. patent application Ser. No. 16/053,763, filed Aug. 2, 2018, issuing as U.S. Pat. No. 11,141,493 on Oct. 12, 2021, which is a continuation-in-part of U.S. patent application Ser. No. 15/667,603, filed Aug. 2, 2017, which is a continuation-in-part of U.S. patent application Ser. No. 14/644,181, filed Mar. 10, 2015, and issued as U.S. Pat. No. 9,938,521 on Apr. 10, 2018, and claims the benefit of U.S. Provisional Appl. No. 61/950,733, filed Mar. 10, 2014; U.S. Provisional Appl. No. 62/036,576, filed Aug. 12, 2014; U.S. Provisional Appl. No. 62/370,202, filed Aug. 2, 2016; U.S. Provisional Appl. No. 62/400,526, filed Sep. 27, 2016; U.S. Provisional Appl. No. 62/443,568, filed Jan. 6, 2017; U.S. Provisional Appl. No. 62/503,800, filed May 9, 2017; and U.S. Provisional Appl. No. 62/535,193, filed Jul. 20, 2017; the contents of which are hereby incorporated by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Sep. 29, 2021, is named SequenceListing.txt and is 1,612,389 bytes in size.

FIELD OF THE INVENTION

The invention relates to CRISPR/CAS-related methods and components for editing of a target nucleic acid sequence, and applications thereof in connection with Leber's Congenital Amaurosis 10 (LCA10).

BACKGROUND

Leber's congenital amaurosis (LCA) is the most severe form of inherited retinal dystrophy, with an onset of disease symptoms in the first years of life (Leber 1869) and an estimated prevalence of approximately 1 in 50,000 worldwide (Koenekoop 2007; Stone 2007). Genetically, LCA is a heterogeneous disease. To date, fifteen genes have been identified with mutations that result in LCA (den Hollander 2008; Estrada-Cuzcano 2011). The CEP290 gene is the most frequently mutated LCA gene accounting for approximately 15% of all cases (Stone 2007; den Hollander 2008; den Hollander 2006; Perrault 2007). Severe mutations in CEP290 have also been reported to cause systemic diseases that are characterized by brain defects, kidney malformations, polydactyly and/or obesity (Baal 2007; den Hollander 2008; Helou 2007; Valente 2006). Mutations of CEP290 are observed in several diseases, including Senior-Loken syndrome, Meckel Gruber syndrome, Bardet-Biedle syndrome, Joubert Syndrome, and Leber Congenital Amaurosis 10 (LCA10). Patients with LCA and early-onset retinal dystrophy often carry hypomorphic CEP290 alleles (Stone 2007; den Hollander 2006; Perrault 2007; Coppieters 2010; Littink 2010).

LCA, and other retinal dystrophies such as Retinitis Pigmentosa (RP), have long been considered incurable diseases. However, the first phase I/II clinical trials using gene augmentation therapy have led to promising results in a selected group of adult LCA/RP patients with mutations in the RPE65 gene (Bainbridge 2008; Cideciyan 2008; Hauswirth 2008; Maguire 2008). Unilateral subretinal injections of adeno-associated virus particles carrying constructs encoding the wild-type RPE65 cDNA were shown to be safe and moderately effective in some patients, without causing any adverse effects. In a follow-up study including adults and children, visual improvements were more sustained, especially in the children all of whom gained ambulatory vision (Maguire 2009). Although these studies demonstrated the potential to treat LCA using gene augmentation therapy and increased the development of therapeutic strategies for other genetic subtypes of retinal dystrophies (den Hollander 2010), it is hard to control the expression levels of the therapeutic genes when using gene augmentation therapy.

LCA10, one type of LCA, is an inherited (autosomal recessive) retinal degenerative disease characterized by severe loss of vision at birth. All subjects having LCA10 have had at least one c.2991+1655A to G (adenine to guanine) mutation in the CEP290 gene. Heterozygous nonsense, frameshift, and splice-site mutations have been identified on the remaining allele. A c.2991+1655A to G mutation in the CEP290 gene give rise to a cryptic splice donor cite in intron 26 which results in the inclusion of an aberrant exon of 128 bp in the mutant CEP290 mRNA, and inserts a premature stop codon (P.C998X). The sequence of the cryptic exon contains part of an Alu repeat.

There are currently no approved therapeutics for LCA10. Despite advances that have been made using gene therapy, there remains a need for therapeutics to treat retinal dystrophies, including LCA10.

SUMMARY OF THE INVENTION

The inventors have addressed a key unmet need in the field by providing new and effective means of delivering genome editing systems to the affected tissues of subjects suffering from CEP290 associated diseases and other inherited retinal dystrophies. This disclosure provides nucleic acids and vectors for efficient transduction of genome editing systems in retinal cells and cells in other tissues, as well as methods of using these vectors to treat subjects. These nucleic acids, vectors and methods represent an important step forward in the development of treatments for CEP290 associated diseases.

In one aspect, the disclosure relates to a method for treating or altering a cell in a subject (e.g., a human subject or an animal subject), that includes administering to the subject a nucleic acid encoding a Cas9 and first and second guide RNAs (gRNAs) targeted to the CEP290 gene of the subject. In certain embodiments, the first and second gRNAs are targeted to one or more target sequences that encompass or are proximal to a CEP290 target position. The first gRNA may include a targeting domain selected from SEQ ID NOs: 389-391 (corresponding RNA sequences in SEQ ID NOs: 530, 468, and 538, respectively), while the second gRNA may include a targeting domain selected from SEQ ID NOs: 388, 392, and 394 (corresponding RNA sequences in SEQ ID NOs: 558, 460, 568, respectively). The Cas9, which may be a modified Cas9 (e.g., a Cas9 engineered to alter PAM specificity, improve fidelity, or to alter or improve another structural or functional aspect of the Cas9), may include one or more of a nuclear localization signal (NLS) and/or a polyadenylation signal. Certain embodiments are characterized by Cas9s that include both a C-terminal and an N-terminal NLS. The Cas9 is encoded, in certain embodiments, by SEQ ID NO: 39, and its expression is optionally driven by one of a CMV, EFS, or hGRK1 promoter, as set out in SEQ ID NOs: 401-403 respectively. The nucleic acid also includes, in various cases, first and second inverted terminal repeat sequences (ITRs).

Continuing with this aspect of the disclosure, a nucleic acid comprising any or all of the features described above may be administered to the subject via an adeno-associated viral (AAV) vector, such as an AAVS vector. The vector may be delivered to the retina of the subject (for example, by subretinal injection). Various embodiments of the method may be used in the treatment of human subjects. For example, the methods may be used to treat subjects suffering from a CEP290 associated disease such as LCA10, to restore CEP290 function in a subject in need thereof, and/or to alter a cell in the subject, such as a retinal cell and/or a photoreceptor cell.

In another aspect, this disclosure relates to a nucleic acid encoding a Cas9, a first gRNA with a targeting domain selected from SEQ ID NOs: 389-391 (corresponding RNA sequences in SEQ ID NOs: 530, 468, and 538, respectively), and a second gRNA with a targeting domain selected from SEQ ID NOs: 388, 392, and 394 (corresponding RNA sequences in SEQ ID NOs: 558, 460, and 568, respectively). The nucleic acid may, in various embodiments, incorporate any or all of the features described above (e.g., the NLS and/or polyadenylation signal; the CMV, EFS or hGRK1 promoter; and/or the ITRs). The nucleic acid may be part of an AAV vector, which vector may be used in medicine, for example to treat a CEP290 associated disease such as LCA10, and/or may be used to edit specific cells including retinal cells, for instance retinal photoreceptor cells. The nucleic acid may also be used for the production of a medicament.

In yet another aspect, this disclosure relates to a method of treating a subject that includes the step of contacting a retina of the subject with one or more recombinant viral vectors (e.g., AAV vectors) that encode a Cas9 and first and second gRNAs. The first and second gRNAs are adapted to form first and second ribonucleoprotein complexes with the Cas9, and the first and second complexes in turn are adapted to cleave first and second target sequences, respectively, on either side of a CEP290 target position as that term is defined below. This cleavage results in the alteration of the nucleic acid sequence of the CEP290 target position. In some embodiments, the step of contacting the retina with one or more recombinant viral vectors includes administering to the retina of the subject, by subretinal injection, a composition comprising the one or more recombinant viral vectors. The alteration of the nucleic acid sequence of the CEP290 target position can include formation of an indel, deletion of part or all of the CEP290 target position, and/or inversion of a nucleotide sequence in the CEP290 target position. The subject, in certain embodiments, is a primate.

The genome editing systems, compositions, and methods of the present disclosure can support high levels of productive editing in retinal cells, e.g., in photoreceptor cells. In certain embodiments, 10%, 15%, 20%, or 25% of retinal cells in samples modified according to the methods of this disclosure (e.g., in retinal samples contacted with a genome editing system of this disclosure) comprise a productive alteration of an allele of the CEP290 gene. A productive alteration may include, variously, a deletion and/or inversion of a sequence comprising an IVS26 mutation, or another modification that results in an increase in the expression of functional CEP290 protein in a cell. In certain embodiments, 25%, 30%, 35%, 40%, 45%, 50%, or more than 50% of photoreceptor cells in retinal samples modified according to the methods of this disclosure (e.g., in retinal samples contacted with a genome editing system of this disclosure) comprise a productive alteration of an allele of the CEP290 gene.

In another aspect, this disclosure relates to a nucleic acid encoding a Cas9 and first and second gRNAs targeted to a CEP290 gene of a subject for use in therapy, e.g. in the treatment of

CEP290-associated disease. The CEP290 associated disease may be, in some embodiments, LCA10, and in other embodiments may be selected from the group consisting of Senior-Loken syndrome, Meckel Gruber syndrome, Bardet-Biedle syndrome and Joubert Syndrome. A targeting domain of the first gRNA may comprise a sequence selected from SEQ ID NOs: 389-391 (corresponding RNA sequences in SEQ ID NOs: 530, 468, and 538, respectively), and a targeting domain of the second gRNA may comprise a sequence selected from SEQ ID NOs: 388, 392, and 394, respectively (corresponding RNA sequences in SEQ ID NOs: 558, 460, and 568, respectively). In certain embodiments, the first and second gRNA targeting domains comprise SEQ ID NOs: 389 and 388, respectively. In other embodiments, the first and second gRNA targeting domains comprise the sequences of SEQ ID NOs: 389 and 392, respectively; SEQ ID NOs: 389 and 394, respectively; SEQ ID NOs: 390 and 388, respectively; SEQ ID NOs: 391 and 388, respectively; or SEQ ID NOs: 391 and 392, respectively. In still other embodiments, the first and second targeting domains comprise the sequences of SEQ ID NOs: 390 and 392, respectively; SEQ ID NOs: 390 and 394, respectively; or SEQ ID NOs: 391 and 394, respectively. The gRNAs according to this aspect of the disclosure may be unimolecular, and may comprise RNA sequences according to SEQ ID NOs: 2779 or 2786 (corresponding to the DNA sequences of SEQ ID NOs: 2785 and 2787, respectively). Alternatively, the gRNAs may be two-part modular gRNAs according to either sequence, where the crRNA component comprises the portion of SEQ ID NO: 2785/2779 or 2787/2786 that is underlined below, and the tracrRNA component comprises the portion that is double-underlined below:

DNA:  (SEQ ID NO: 2785) [N] ₁₆₋₂₄GTTTTAGTACTCTGGAAACAGAATCTACTAAAACAAGGCAAA ATGCCGTGTTTATCTCGTCAACTTGTTGGCGAGATTTTTT and RNA:  (SEQ ID NO: 2779) [N] ₁₆₋₂₄GUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGCAAA AUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUUUU. DNA:  (SEQ ID NO: 2787) [N] ₁₆₋₂₄GTTATAGTACTCTGGAAACAGAATCTACTATAACAAGGCAAA ATGCCGTGTTTATCTCGTCAACTTGTTGGCGAGATTTTTT and RNA:  (SEQ ID NO: 2786) [N] ₁₆₋₂₄GUUAUAGUACUCUGGAAACAGAAUCUACUAUAACAAGGCAAA AUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUUUU.

Continuing with this aspect of the disclosure, the Cas9 encoded by the nucleic acid is, in certain embodiments, a Staphylococcus aureus Cas9, which may be encoded by a sequence comprising SEQ ID NO: 39, or having at least 80%, 85%, 90%, 95% or 99% sequence identity thereto. The Cas9 encoded by the nucleic acid may comprise the amino acid sequence of SEQ ID NO: 26 or may share at least 80%, 85%, 90%, 95% or 99% sequence identity therewith. The Cas9 may be modified in some instances, for example to include one or more nuclear localization signals (NLSs) (e.g., a C-terminal and an N-terminal NLS) and/or a polyadenylation signal. Cas9 expression may be driven by a promoter sequence such as the promoter sequence comprising SEQ ID NO: 401, the promoter sequence comprising SEQ ID NO: 402, or the promoter sequence comprising SEQ ID NO: 403.

Staying with this aspect of the disclosure, the promoter sequence for driving the expression of the Cas9 comprises, in certain embodiments, the sequence of a human GRK1 promoter. In other embodiments, the promoter comprises the sequence of a cytomegalovirus (CMV) promoter or an EFS promoter. For example, the nucleic acid may comprise, in various embodiments, (a) a CMV promoter for Cas9 and gRNAs comprising (or differing by no more than 3 nucleotides from) targeting domains according to SEQ ID NOs: 389 and 392, or (b) a CMV promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 394, or c) a CMV promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 388, or d) a CMV promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 388, or e) a CMV promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 392, or f) an EFS promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 392, or g) an EFS promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 394, or h) an EFS promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 388, or i) an EFS promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 388, or j) an EFS promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 392, or k) an hGRK1 promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 392, or g) an hGRK1promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 394, or h) an hGRK1promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 388, or i) an hGRK1 promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 388, or j) an hGRK1promoter for Cas9 and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 392. In other embodiments, the nucleic acid comprises a CMV promoter and guide RNA targeting sequences according to SEQ ID NOs: 389 and 388. In still other embodiments, the nucleic acid comprises an hGRK promoter and guide RNA targeting sequences according to SEQ ID NOs: 390 and 392, or it comprises a CMV promoter and guide RNA targeting sequences according to SEQ ID NOs: 390 and 392, or an hGRK promoter and guide RNA targeting sequences according to SEQ ID NOs: 390 and 394, or it comprises a CMV promoter and guide RNA targeting sequences according to SEQ ID NOs: 391 and 394, or an hGRK promoter and guide RNA targeting sequences according to SEQ ID NOs: 391 and 394, or it comprises a CMV promoter and guide RNA targeting sequences according to SEQ ID NOs: 390 and 392. And in further embodiments, the promoter is hGRK or CMV while the first and second gRNA targeting domains comprise the sequences of SEQ ID NOs: 389 and 392, SEQ ID NOs: 389 and 394, SEQ ID NOs: 390 and 388, SEQ ID NOs: 391 and 388, or SEQ ID NOs: 391 and 392.

In another aspect, the present disclosure relates to adeno-associated virus (AAV) vectors comprising the nucleic acids described above. AAV vectors comprising the foregoing nucleic acids may be administered to a variety of tissues of a subject, though in certain embodiments the AAV vectors are administered to a retina of the subject, and/or are administered by subretinal injection. The AAV vector may comprise an AAV5 capsid.

An additional aspect of this disclosure relates to a nucleic acid as described above, for delivery via an AAV vector also as described above. The nucleic acid includes in some embodiments, first and second inverted terminal repeat sequences (ITRs), a first guide RNA comprising a targeting domain sequence selected from SEQ ID NOs: 389-391 (corresponding RNA sequences in SEQ ID NOs: 530, 468, and 538, respectively), a second guide RNA comprising a targeting domain sequence selected from SEQ ID NOs: 388, 392, and 394 (corresponding RNA sequences in SEQ ID NOs: 558, 460, and 568, respectively), and a promoter for driving Cas9 expression comprising a sequence selected from SEQ ID NOs: 401-403. In certain embodiments, the nucleic acid includes first and second ITRs and first and second guide RNAs comprising a guide RNA sequence selected from SEQ ID NOs: 2785 and 2787 (e.g., both first and second guide RNAs comprise the sequence of SEQ ID NO: 2787). The nucleic acid may be used in the treatment of human subjects, and/or in the production of a medicament.

The nucleic acids and vectors according to these aspects of the disclosure may be used in medicine, for instance in the treatment of disease. In some embodiments, they are used in the treatment of a CEP290-associated disease, in the treatment of LCA10, or in the treatment of one or more of the following: Senior-Loken syndrome, Meckel Gruber syndrome, Bardet-Biedle syndrome, and/or Joubert Syndrome. Without wishing to be bound by theory, it is contemplated that the nucleic acids and vectors disclosed herein may be used to treat other inherited retinal diseases by adapting the gRNA targeting domains to target and alter the gene of interest. In certain embodiments, the nucleic acids and vectors according to the disclosure may be used for the treatment of other inherited retinal diseases as set forth in Stone 2017, which is incorporated by reference herein in its entirety. For example, in certain embodiments, the nucleic acids and vectors disclosed herein may be used to treat USH2A-related disorders by including gRNAs comprising targeting domains that alter the USH2A gene. Vectors and nucleic acids according to this disclosure may be administered to the retina of a subject, for instance by subretinal injection.

This disclosure also relates to recombinant viral vectors comprising the nucleic acids described above, and to the use of such viral vectors in the treatment of disease. In some embodiments, one or more viral vectors encodes a Cas9, a first gRNA and a second gRNA for use in a method of altering a nucleotide sequence of a CEP 290 target position wherein (a) the first and second gRNAs are adapted to form first and second ribonucleoprotein complexes with the Cas9, and (b) the first and second ribonucleoprotein complexes are adapted to cleave first and second cellular nucleic acid sequences on first and second sides of a CEP290 target position, thereby altering a nucleotide sequence of the CEP290 target position. In use, the one or more recombinant viral vectors is contacted to the retina of a subject, for instance by subretinal injection.

Another aspect of this disclosure relates to AAV vectors, AAV vector genomes and/or nucleic acids that may be carried by AAV vectors, which encode one or more guide RNAs, each comprising a sequence selected from—or having at least 90% sequence identity to—one of SEQ ID NOs: 2785 or 2787, a sequence encoding a Cas9 and a promoter sequence operably coupled to the Cas9 coding sequence, which promoter sequence comprises a sequence selected from—or having at least 90% sequence identity to—one of SEQ ID NOs: 401-403. The Cas9 coding sequence may comprise the sequence of SEQ ID NO: 39, or it may share at least 90% sequence identity therewith. Alternatively or additionally, the Cas9 coding sequence may encode an amino acid sequence comprising SEQ ID NO: 26, or sharing at least 90% sequence identity therewith. In certain embodiments, the AAV vector, vector genome or nucleic acid further comprises one or more of the following: left and right ITR sequences, optionally selected from—or having at least 90% sequence identity to—SEQ ID NOs: 408 and 437, respectively; and one or more U6 promoter sequences operably coupled to the one or more guide RNA sequences. The U6 promoter sequences may comprise, or share at least 90% sequence identity with, SEQ ID NO: 417.

Methods and compositions discussed herein, provide for treating or delaying the onset or progression of diseases of the eye, e.g., disorders that affect retinal cells, e.g., photoreceptor cells.

Methods and compositions discussed herein, provide for treating or delaying the onset or progression of Leber's Congenital Amaurosis 10 (LCA10), an inherited retinal degenerative disease characterized by severe loss of vision at birth. LCA10 is caused by a mutation in the CEP290 gene, e.g., a c.2991+1655A to G (adenine to guanine) mutation in the CEP290 gene which gives rise to a cryptic splice site in intron 26. This is a mutation at nucleotide 1655 of intron 26 of CEP290, e.g., an A to G mutation. CEP290 is also known as: CT87; MKS4; POC3; rd16; BBS14; JBTS5; LCA10; NPHP6; SLSN6; and 3H11Ag.

Methods and compositions discussed herein, provide for treating or delaying the onset or progression of LCA10 by gene editing, e.g., using CRISPR-Cas9 mediated methods to alter a LCA10 target position, as disclosed below.

“LCA10 target position” as used herein refers to nucleotide 1655 of intron 26 of the CEP290 gene, and the mutation at that site that gives rise to a cryptic splice donor site in intron 26 which results in the inclusion of an aberrant exon of 128 bp (c.2991+1523 to c.2991+1650) in the mutant CEP290 mRNA, and inserts a premature stop codon (p.C998X). The sequence of the cryptic exon contains part of an Alu repeat region. The Alu repeats span from c.2991+1162 to c.2991+1638. In an embodiment, the LCA10 target position is occupied by an adenine (A) to guanine (G) mutation (c.2991+1655A to G).

In one aspect, methods and compositions discussed herein, provide for altering a LCA10 target position in the CEP290 gene. The methods and compositions described herein introduce one or more breaks near the site of the LCA target position (e.g., c.2991+1655A to G) in at least one allele of the CEP290 gene. Altering the LCA10 target position refers to (1) break-induced introduction of an indel (also referred to herein as NHEJ-mediated introduction of an indel) in close proximity to or including a LCA10 target position (e.g., c.2991+1655A to G), or (2) break-induced deletion (also referred to herein as NHEJ-mediated deletion) of genomic sequence including the mutation at a LCA10 target position (e.g., c.2991+1655A to G). Both approaches give rise to the loss or destruction of the cryptic splice site resulting from the mutation at the LCA10 target position (e.g., c.2991+1655A to G).

In an embodiment, a single strand break is introduced in close proximity to or at the LCA10 target position (e.g., c.2991+1655A to G) in the CEP290 gene. While not wishing to be bound by theory, it is believed that break-induced indels (e.g., indels created following NHEJ) destroy the cryptic splice site. In an embodiment, the single strand break will be accompanied by an additional single strand break, positioned by a second gRNA molecule.

In an embodiment, a double strand break is introduced in close proximity to or at the LCA10 target position (e.g., c.2991+1655A to G) in the CEP290 gene. While not wishing to be bound by theory, it is believed that break-induced indels (e.g., indels created following NHEJ) destroy the cryptic splice site. In an embodiment, a double strand break will be accompanied by an additional single strand break may be positioned by a second gRNA molecule. In an embodiment, a double strand break will be accompanied by two additional single strand breaks positioned by a second gRNA molecule and a third gRNA molecule.

In an embodiment, a pair of single strand breaks is introduced in close proximity to or at the LCA10 target position (e.g., c.2991+1655A to G) in the CEP290 gene. While not wishing to be bound by theory, it is believed that break-induced indels destroy the cryptic splice site. In an embodiment, the pair of single strand breaks will be accompanied by an additional double strand break, positioned by a third gRNA molecule. In an embodiment, the pair of single strand breaks will be accompanied by an additional pair of single strand breaks positioned by a third gRNA molecule and a fourth gRNA molecule.

In an embodiment, two double strand breaks are introduced to flank the LCA10 target position in the CEP290 gene (one 5′ and the other one 3′ to the mutation at the LCA10 target position, e.g., c.2991+1655A to G) to remove (e.g., delete) the genomic sequence including the mutation at the LCA10 target position. It is contemplated herein that in an embodiment the break-induced deletion of the genomic sequence including the mutation at the LCA10 target position is mediated by NHEJ. In an embodiment, the breaks (i.e., the two double strand breaks) are positioned to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat. The breaks, i.e., two double strand breaks, can be positioned upstream and downstream of the LCA10 target position, as discussed herein.

In an embodiment, one double strand break (either 5′ or 3′ to the mutation at the LCA10 target position, e.g., c.2991+1655A to G) and two single strand breaks (on the other side of the mutation at the LCA10 target position from the double strand break) are introduced to flank the LCA10 target position in the CEP290 gene to remove (e.g., delete) the genomic sequence including the mutation at the LCA10 target position. It is contemplated herein that in an embodiment the break-induced deletion of the genomic sequence including the mutation at the LCA10 target position is mediated by NHEJ. In an embodiment, the breaks (i.e., the double strand break and the two single strand breaks) are positioned to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat. The breaks, e.g., one double strand break and two single strand breaks, can be positioned upstream and downstream of the LCA10 target position, as discussed herein.

In an embodiment, two pairs of single strand breaks (two 5′ and the other two 3′ to the mutation at the LCA10 target position, e.g., c.2991+1655A to G) are introduced to flank the LCA10 target position in the CEP290 gene to remove (e.g., delete) the genomic sequence including the mutation at the LCA10 target position. It is contemplated herein that in an embodiment the break-induced deletion of the genomic sequence including the mutation at the LCA10 target position is mediated by NHEJ. In an embodiment, the breaks (e.g., two pairs of single strand breaks) are positioned to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat. The breaks, e.g., two pairs of single strand breaks, can be positioned upstream or downstream of the LCA10 target position, as discussed herein.

The LCA10 target position may be targeted by cleaving with either a single nuclease or dual nickases, e.g., to induce break-induced indel in close proximity to or including the LCA10 target position or break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene. The method can include acquiring knowledge of the mutation carried by the subject, e.g., by sequencing the appropriate portion of the CEP290 gene.

In one aspect, disclosed herein is a gRNA molecule, e.g., an isolated or non-naturally occurring gRNA molecule, comprising a targeting domain which is complementary with a target domain from the CEP290 gene.

When two or more gRNAs are used to position two or more cleavage events, e.g., double strand or single strand breaks, in a target nucleic acid, it is contemplated that in an embodiment the two or more cleavage events may be made by the same or different Cas9 proteins. For example, when two gRNAs are used to position two double strand breaks, a single Cas9 nuclease may be used to create both double strand breaks. When two or more gRNAs are used to position two or more single stranded breaks (single strand breaks), a single Cas9 nickase may be used to create the two or more single strand breaks. When two or more gRNAs are used to position at least one double strand break and at least one single strand break, two Cas9 proteins may be used, e.g., one Cas9 nuclease and one Cas9 nickase. It is contemplated that in an embodiment when two or more Cas9 proteins are used that the two or more Cas9 proteins may be delivered sequentially to control specificity of a double strand versus a single strand break at the desired position in the target nucleic acid.

In some embodiments, the targeting domain of the first gRNA molecule and the targeting domain of the second gRNA molecule hybridize to the target domain from the target nucleic acid molecule (i.e., the CEP290 gene) through complementary base pairing to opposite strands of the target nucleic acid molecule. In some embodiments, the first gRNA molecule and the second gRNA molecule are configured such that the PAMs are oriented outward.

In an embodiment, the targeting domain of a gRNA molecule is configured to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat, or the endogenous CEP290 splice sites, in the target domain. The gRNA molecule may be a first, second, third and/or fourth gRNA molecule.

In an embodiment, the targeting domain of a gRNA molecule is configured to position a cleavage event sufficiently far from a preselected nucleotide, e.g., the nucleotide of a coding region, such that the nucleotide is not altered. In an embodiment, the targeting domain of a gRNA molecule is configured to position an intronic cleavage event sufficiently far from an intron/exon border, or naturally occurring splice signal, to avoid alteration of the exonic sequence or unwanted splicing events. The gRNA molecule may be a first, second, third and/or fourth gRNA molecule, as described herein.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Table 11. In some embodiments, the targeting domain is selected from those in Table 11. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 387) GACACTGCCAATAGGGATAGGT; (SEQ ID NO: 388) GTCAAAAGCTACCGGTTACCTG; (SEQ ID NO: 389) GTTCTGTCCTCAGTAAAAGGTA; (SEQ ID NO: 390) GAATAGTTTGTTCTGGGTAC; (SEQ ID NO: 391) GAGAAAGGGATGGGCACTTA; (SEQ ID NO: 392) GATGCAGAACTAGTGTAGAC; (SEQ ID NO: 393) GTCACATGGGAGTCACAGGG; or (SEQ ID NO: 394) GAGTATCTCCTGTTTGGCA.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Table 11. In an embodiment, the two or more gRNAs or targeting domains are selected from one or more of the pairs of gRNAs or targeting domains described herein, e.g., as indicated in Table 11. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Table 11.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Table 2A-2D. In some embodiments, the targeting domain is selected from those in Table 2A-2D. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 395) GAGAUACUCACAAUUACAAC; or (SEQ ID NO: 396) GAUACUCACAAUUACAACUG.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 2A-2D. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 2A-2D.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Tables 3A-3C. In some embodiments, the targeting domain is selected from those in Tables 3A-3C. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 395) GAGAUACUCACAAUUACAAC; or (SEQ ID NO: 397) GAUACUCACAAUUACAA.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single stranded breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 3A-3C. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 3A-3C.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Tables 7A-7D. In some embodiments, the targeting domain is selected from those in Tables 7A-7D. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 398) GCACCUGGCCCCAGUUGUAAUU.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single stranded breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 7A-7D. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 7A-7D.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Tables 4A-4D. In some embodiments, the targeting domain is selected from those in Tables 4A-4D. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 457) GCUACCGGUUACCUGAA; (SEQ ID NO: 458) GCAGAACUAGUGUAGAC; (SEQ ID NO: 459) GUUGAGUAUCUCCUGUU; (SEQ ID NO: 460) GAUGCAGAACUAGUGUAGAC; or (SEQ ID NO: 461) GCUUGAACUCUGUGCCAAAC.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single stranded breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 4A-4D. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 4A-4D.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Tables 8A-8D. In some embodiments, the targeting domain is selected from those in Tables 8A-8D. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 457) GCUACCGGUUACCUGAA; (SEQ ID NO: 458) GCAGAACUAGUGUAGAC; (SEQ ID NO: 459) GUUGAGUAUCUCCUGUU; (SEQ ID NO: 460) GAUGCAGAACUAGUGUAGAC; (SEQ ID NO: 461) GCUUGAACUCUGUGCCAAAC; (SEQ ID NO: 462) GAAAGAUGAAAAAUACUCUU; (SEQ ID NO: 463) GAAAUAGAUGUAGAUUG; (SEQ ID NO: 464) GAAAUAUUAAGGGCUCUUCC; (SEQ ID NO: 465) GAACAAAAGCCAGGGACCAU; (SEQ ID NO: 466) GAACUCUAUACCUUUUACUG; (SEQ ID NO: 467) GAAGAAUGGAAUAGAUAAUA; (SEQ ID NO: 468) GAAUAGUUUGUUCUGGGUAC; (SEQ ID NO: 469) GAAUGGAAUAGAUAAUA; (SEQ ID NO: 470) GAAUUUACAGAGUGCAUCCA; (SEQ ID NO: 471) GAGAAAAAGGAGCAUGAAAC; (SEQ ID NO: 472) GAGAGCCACAGUGCAUG; (SEQ ID NO: 473) GAGGUAGAAUCAAGAAG; (SEQ ID NO: 474) GAGUGCAUCCAUGGUCC; (SEQ ID NO: 475) GAUAACUACAAAGGGUC; (SEQ ID NO: 476) GAUAGAGACAGGAAUAA; (SEQ ID NO: 477) GAUGAAAAAUACUCUUU; (SEQ ID NO: 478) GAUGACAUGAGGUAAGU; (SEQ ID NO: 479) GCAUGUGGUGUCAAAUA; (SEQ ID NO: 480) GCCUGAACAAGUUUUGAAAC; (SEQ ID NO: 481) GCUCUUUUCUAUAUAUA; (SEQ ID NO: 482) GCUUUUGACAGUUUUUAAGG; (SEQ ID NO: 483) GCUUUUGUUCCUUGGAA; (SEQ ID NO: 484) GGAACAAAAGCCAGGGACCA; (SEQ ID NO: 485) GGACUUGACUUUUACCCUUC; (SEQ ID NO: 486) GGAGAAUAGUUUGUUCU; (SEQ ID NO: 487) GGAGUCACAUGGGAGUCACA; (SEQ ID NO: 488) GGAUAGGACAGAGGACA; (SEQ ID NO: 489) GGCUGUAAGAUAACUACAAA; (SEQ ID NO: 490) GGGAGAAUAGUUUGUUC; (SEQ ID NO: 491) GGGAGUCACAUGGGAGUCAC; (SEQ ID NO: 492) GGGCUCUUCCUGGACCA; (SEQ ID NO: 493) GGGUACAGGGGUAAGAGAAA; (SEQ ID NO: 494) GGUCCCUGGCUUUUGUUCCU; (SEQ ID NO: 495) GUAAAGGUUCAUGAGACUAG; (SEQ ID NO: 496) GUAACAUAAUCACCUCUCUU; (SEQ ID NO: 497) GUAAGACUGGAGAUAGAGAC; (SEQ ID NO: 498) GUACAGGGGUAAGAGAA; (SEQ ID NO: 499) GUAGCUUUUGACAGUUUUUA; (SEQ ID NO: 500) GUCACAUGGGAGUCACA; (SEQ ID NO: 501) GUGGAGAGCCACAGUGCAUG; (SEQ ID NO: 502) GUUACAAUCUGUGAAUA; (SEQ ID NO: 503) GUUCUGUCCUCAGUAAA; (SEQ ID NO: 504) GUUUAGAAUGAUCAUUCUUG; (SEQ ID NO: 505) GUUUGUUCUGGGUACAG; (SEQ ID NO: 506) UAAAAACUGUCAAAAGCUAC; (SEQ ID NO: 507) UAAAAGGUAUAGAGUUCAAG; (SEQ ID NO: 508) UAAAUCAUGCAAGUGACCUA; or (SEQ ID NO: 509) UAAGAUAACUACAAAGGGUC.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single stranded breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 8A-8D. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 8A-8D.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Table 5A-5D. In some embodiments, the targeting domain is selected from those in Table 5A-5D. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 510) GAAUCCUGAAAGCUACU.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single stranded breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 5A-5D. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 5A-5D.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Tables 9A-9E. In some embodiments, the targeting domain is selected from those in Tables 9A-9E. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 460) GAUGCAGAACUAGUGUAGAC; (SEQ ID NO: 468) GAAUAGUUUGUUCUGGGUAC; (SEQ ID NO: 480) GCCUGAACAAGUUUUGAAAC; (SEQ ID NO: 494) GGUCCCUGGCUUUUGUUCCU; (SEQ ID NO: 497) GUAAGACUGGAGAUAGAGAC; (SEQ ID NO: 511) GCUAAAUCAUGCAAGUGACCUAAG; (SEQ ID NO: 512) GGUCACUUGCAUGAUUUAG; (SEQ ID NO: 513) GUCACUUGCAUGAUUUAG; (SEQ ID NO: 514) GCCUAGGACUUUCUAAUGCUGGA; (SEQ ID NO: 515) GGACUUUCUAAUGCUGGA; (SEQ ID NO: 516) GGGACCAUGGGAGAAUAGUUUGUU; (SEQ ID NO: 517) GGACCAUGGGAGAAUAGUUUGUU; (SEQ ID NO: 518) GACCAUGGGAGAAUAGUUUGUU; (SEQ ID NO: 519) GGUCCCUGGCUUUUGUUCCUUGGA; (SEQ ID NO: 520) GUCCCUGGCUUUUGUUCCUUGGA; (SEQ ID NO: 521) GAAAACGUUGUUCUGAGUAGCUUU; (SEQ ID NO: 522) GUUGUUCUGAGUAGCUUU; (SEQ ID NO: 523) GUCCCUGGCUUUUGUUCCU; (SEQ ID NO: 524) GACAUCUUGUGGAUAAUGUAUCA; (SEQ ID NO: 525) GUCCUAGGCAAGAGACAUCUU; (SEQ ID NO: 526) GCCAGCAAAAGCUUUUGAGCUAA; (SEQ ID NO: 527) GCAAAAGCUUUUGAGCUAA; (SEQ ID NO: 528) GAUCUUAUUCUACUCCUGUGA; (SEQ ID NO: 529) GCUUUCAGGAUUCCUACUAAAUU; (SEQ ID NO: 530) GUUCUGUCCUCAGUAAAAGGUA; (SEQ ID NO: 531) GAACAACGUUUUCAUUUA; (SEQ ID NO: 532) GUAGAAUAUCAUAAGUUACAAUCU; (SEQ ID NO: 533) GAAUAUCAUAAGUUACAAUCU; (SEQ ID NO: 534) GUGGCUGUAAGAUAACUACA; (SEQ ID NO: 535) GGCUGUAAGAUAACUACA; (SEQ ID NO: 536) GUUUAACGUUAUCAUUUUCCCA; (SEQ ID NO: 537) GUAAGAGAAAGGGAUGGGCACUUA; (SEQ ID NO: 538) GAGAAAGGGAUGGGCACUUA; (SEQ ID NO: 539) GAAAGGGAUGGGCACUUA; (SEQ ID NO: 540) GUAAAUGAAAACGUUGUU; (SEQ ID NO: 541) GAUAAACAUGACUCAUAAUUUAGU; (SEQ ID NO: 542) GGAACAAAAGCCAGGGACCAUGG; (SEQ ID NO: 543) GAACAAAAGCCAGGGACCAUGG; (SEQ ID NO: 544) GGGAGAAUAGUUUGUUCUGGGUAC; (SEQ ID NO: 545) GGAGAAUAGUUUGUUCUGGGUAC; (SEQ ID NO: 546) GAGAAUAGUUUGUUCUGGGUAC; (SEQ ID NO: 547) GAAAUAGAGGCUUAUGGAUU; (SEQ ID NO: 548) GUUCUGGGUACAGGGGUAAGAGAA; (SEQ ID NO: 549) GGGUACAGGGGUAAGAGAA; (SEQ ID NO: 550) GGUACAGGGGUAAGAGAA; (SEQ ID NO: 551) GUAAAUUCUCAUCAUUUUUUAUUG; (SEQ ID NO: 552) GGAGAGGAUAGGACAGAGGACAUG; (SEQ ID NO: 553) GAGAGGAUAGGACAGAGGACAUG; (SEQ ID NO: 554) GAGGAUAGGACAGAGGACAUG; (SEQ ID NO: 555) GGAUAGGACAGAGGACAUG; (SEQ ID NO: 556) GAUAGGACAGAGGACAUG; (SEQ ID NO: 557) GAAUAAAUGUAGAAUUUUAAUG; (SEQ ID NO: 558) GUCAAAAGCUACCGGUUACCUG; (SEQ ID NO: 559) GUUUUUAAGGCGGGGAGUCACAU; (SEQ ID NO: 560) GUCUUACAUCCUCCUUACUGCCAC; (SEQ ID NO: 561) GAGUCACAGGGUAGGAUUCAUGUU; (SEQ ID NO: 562) GUCACAGGGUAGGAUUCAUGUU; (SEQ ID NO: 563) GGCACAGAGUUCAAGCUAAUACAU; (SEQ ID NO: 564) GCACAGAGUUCAAGCUAAUACAU; (SEQ ID NO: 565) GAGUUCAAGCUAAUACAU; (SEQ ID NO: 566) GUGUUGAGUAUCUCCUGUUUGGCA; (SEQ ID NO: 567) GUUGAGUAUCUCCUGUUUGGCA; (SEQ ID NO: 568) GAGUAUCUCCUGUUUGGCA; (SEQ ID NO: 569) GAAAAUCAGAUUUCAUGUGUG; (SEQ ID NO: 570) GCCACAAGAAUGAUCAUUCUAAAC; (SEQ ID NO: 571) GGCGGGGAGUCACAUGGGAGUCA; (SEQ ID NO: 572) GCGGGGAGUCACAUGGGAGUCA; (SEQ ID NO: 573) GGGGAGUCACAUGGGAGUCA; (SEQ ID NO: 574) GGGAGUCACAUGGGAGUCA; (SEQ ID NO: 575) GGAGUCACAUGGGAGUCA; (SEQ ID NO: 576) GCUUUUGACAGUUUUUAAGGCG; (SEQ ID NO: 577) GAUCAUUCUUGUGGCAGUAAG; (SEQ ID NO: 578) GAGCAAGAGAUGAACUAG; (SEQ ID NO: 579) GUAGAUUGAGGUAGAAUCAAGAA; (SEQ ID NO: 580) GAUUGAGGUAGAAUCAAGAA; (SEQ ID NO: 581) GGAUGUAAGACUGGAGAUAGAGAC; (SEQ ID NO: 582) GAUGUAAGACUGGAGAUAGAGAC; (SEQ ID NO: 583) GGGAGUCACAUGGGAGUCACAGGG; (SEQ ID NO: 584) GGAGUCACAUGGGAGUCACAGGG; (SEQ ID NO: 585) GAGUCACAUGGGAGUCACAGGG; (SEQ ID NO: 586) GUCACAUGGGAGUCACAGGG; (SEQ ID NO: 587) GUUUACAUAUCUGUCUUCCUUAA; or (SEQ ID NO: 588) GAUUUCAUGUGUGAAGAA.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single stranded breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 9A-9E. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 9A-9E.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Tables 6A-6B. In some embodiments, the targeting domain is selected from those in Tables 6A-6B. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 589) GAGUUCAAGCUAAUACAUGA; (SEQ ID NO: 590) GUUGUUCUGAGUAGCUU; or (SEQ ID NO: 591) GGCAAAAGCAGCAGAAAGCA.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single stranded breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 6A-6B. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 6A-6B.

In an embodiment, the LCA10 target position in the CEP290 gene is targeted. In an embodiment, the targeting domain comprises a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from Tables 10A-10B. In some embodiments, the targeting domain is selected from those in Tables 10A-10B. For example, in certain embodiments, the targeting domain is:

(SEQ ID NO: 589) GAGUUCAAGCUAAUACAUGA; (SEQ ID NO: 590) GUUGUUCUGAGUAGCUU; (SEQ ID NO: 591) GGCAAAAGCAGCAGAAAGCA; (SEQ ID NO: 592) GUGGCUGAAUGACUUCU; or (SEQ ID NO: 593) GACUAGAGGUCACGAAA.

In an embodiment, when two or more gRNAs are used to position two or more breaks, e.g., two or more single stranded breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 10A-10B. In an embodiment, when two or more gRNAs are used to position four breaks, e.g., four single strand breaks in the target nucleic acid sequence, each guide RNA is independently selected from one of Tables 10A-10B.

In an embodiment, the gRNA, e.g., a gRNA comprising a targeting domain, which is complementary with a target domain from the CEP290 gene, is a modular gRNA. In other embodiments, the gRNA is a chimeric gRNA.

In an embodiment, when two gRNAs are used to position two breaks, e.g., two single strand breaks, in the target nucleic acid sequence, each guide RNA is independently selected from one or more of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11.

In an embodiment, the targeting domain which is complementary with a target domain from the CEP290 gene comprises 16 or more nucleotides in length. In an embodiment, the targeting domain which is complementary with a target domain from the CEP290 gene is 16 nucleotides or more in length. In an embodiment, the targeting domain is 16 nucleotides in length. In an embodiment, the targeting domain is 17 nucleotides in length. In an embodiment, the targeting domain is 18 nucleotides in length. In an embodiment, the targeting domain is 19 nucleotides in length. In an embodiment, the targeting domain is 20 nucleotides in length. In an embodiment, the targeting domain is 21 nucleotides in length. In an embodiment, the targeting domain is 22 nucleotides in length. In an embodiment, the targeting domain is 23 nucleotides in length. In an embodiment, the targeting domain is 24 nucleotides in length. In an embodiment, the targeting domain is 25 nucleotides in length. In an embodiment, the targeting domain is 26 nucleotides in length.

In an embodiment, the targeting domain comprises 16 nucleotides.

In an embodiment, the targeting domain comprises 17 nucleotides.

In an embodiment, the targeting domain comprises 18 nucleotides.

In an embodiment, the targeting domain comprises 19 nucleotides.

In an embodiment, the targeting domain comprises 20 nucleotides.

In an embodiment, the targeting domain comprises 21 nucleotides.

In an embodiment, the targeting domain comprises 22 nucleotides.

In an embodiment, the targeting domain comprises 23 nucleotides.

In an embodiment, the targeting domain comprises 24 nucleotides.

In an embodiment, the targeting domain comprises 25 nucleotides.

In an embodiment, the targeting domain comprises 26 nucleotides.

A gRNA as described herein may comprise from 5′ to 3′: a targeting domain (comprising a “core domain”, and optionally a “secondary domain”); a first complementarity domain; a linking domain; a second complementarity domain; a proximal domain; and a tail domain. In some embodiments, the proximal domain and tail domain are taken together as a single domain.

In an embodiment, a gRNA comprises a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 20 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In another embodiment, a gRNA comprises a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 30 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In another embodiment, a gRNA comprises a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 30 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In another embodiment, a gRNA comprises a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 40 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

A cleavage event, e.g., a double strand or single strand break, is generated by a Cas9 molecule. The Cas9 molecule may be an enzymatically active Cas9 (eaCas9) molecule, e.g., an eaCas9 molecule that forms a double strand break in a target nucleic acid or an eaCas9 molecule forms a single strand break in a target nucleic acid (e.g., a nickase molecule).

In an embodiment, the eaCas9 molecule catalyzes a double strand break.

In some embodiments, the eaCas9 molecule comprises HNH-like domain cleavage activity but has no, or no significant, N-terminal RuvC-like domain cleavage activity. In this case, the eaCas9 molecule is an HNH-like domain nickase, e.g., the eaCas9 molecule comprises a mutation at D10, e.g., D10A. In other embodiments, the eaCas9 molecule comprises N-terminal RuvC-like domain cleavage activity but has no, or no significant, HNH-like domain cleavage activity. In an embodiment, the eaCas9 molecule is an N-terminal RuvC-like domain nickase, e.g., the eaCas9 molecule comprises a mutation at H840, e.g., H840A. In an embodiment, the eaCas9 molecule is an N-terminal RuvC-like domain nickase, e.g., the eaCas9 molecule comprises a mutation at H863, e.g., H863A.

In an embodiment, a single strand break is formed in the strand of the target nucleic acid to which the targeting domain of said gRNA is complementary. In another embodiment, a single strand break is formed in the strand of the target nucleic acid other than the strand to which the targeting domain of said gRNA is complementary.

In another aspect, disclosed herein is a nucleic acid, e.g., an isolated or non-naturally occurring nucleic acid, e.g., DNA, that comprises (a) a sequence that encodes a gRNA molecule comprising a targeting domain that is complementary with a target domain in CEP290 gene as disclosed herein.

In an embodiment, the nucleic acid encodes a gRNA molecule, e.g., the first gRNA molecule, comprising a targeting domain comprising a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from any one of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. In an embodiment, the nucleic acid encodes a gRNA molecule comprising a targeting domain that is selected from those in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11.

In an embodiment, the nucleic acid encodes a modular gRNA, e.g., one or more nucleic acids encode a modular gRNA. In other embodiments, the nucleic acid encodes a chimeric gRNA. The nucleic acid may encode a gRNA, e.g., the first gRNA molecule, comprising a targeting domain comprising 16 nucleotides or more in length. In one embodiment, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 16 nucleotides in length. In other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 17 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 18 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 19 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 20 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 21 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 22 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 23 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 24 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 25 nucleotides in length. In still other embodiments, the nucleic acid encodes a gRNA, e.g., the first gRNA molecule, comprising a targeting domain that is 26 nucleotides in length.

In an embodiment, a nucleic acid encodes a gRNA comprising from 5′ to 3′ : a targeting domain (comprising a “core domain”, and optionally a “secondary domain”); a first complementarity domain; a linking domain; a second complementarity domain; a proximal domain; and a tail domain. In some embodiments, the proximal domain and tail domain are taken together as a single domain.

In an embodiment, a nucleic acid encodes a gRNA e.g., the first gRNA molecule, comprising a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 20 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, a nucleic acid encodes a gRNA e.g., the first gRNA molecule, comprising a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 30 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, a nucleic acid encodes a gRNA e.g., the first gRNA molecule, comprising a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 30 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, a nucleic acid encodes a gRNA comprising e.g., the first gRNA molecule, a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 40 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, a nucleic acid comprises (a) a sequence that encodes a gRNA molecule comprising a targeting domain that is complementary with a target domain in the CEP290 gene as disclosed herein, and further comprises (b) a sequence that encodes a Cas9 molecule.

The Cas9 molecule may be a nickase molecule, a enzymatically activating Cas9 (eaCas9) molecule, e.g., an eaCas9 molecule that forms a double strand break in a target nucleic acid and an eaCas9 molecule forms a single strand break in a target nucleic acid. In an embodiment, a single strand break is formed in the strand of the target nucleic acid to which the targeting domain of said gRNA is complementary. In another embodiment, a single strand break is formed in the strand of the target nucleic acid other than the strand to which the targeting domain of said gRNA is complementary.

In an embodiment, the eaCas9 molecule catalyzes a double strand break.

In some embodiments, the eaCas9 molecule comprises HNH-like domain cleavage activity but has no, or no significant, N-terminal RuvC-like domain cleavage activity. In other embodiments, the said eaCas9 molecule is an HNH-like domain nickase, e.g., the eaCas9 molecule comprises a mutation at D10, e.g., D1OA. In other embodiments, the eaCas9 molecule comprises N-terminal RuvC-like domain cleavage activity but has no, or no significant, HNH-like domain cleavage activity. In another embodiment, the eaCas9 molecule is an N-terminal RuvC-like domain nickase, e.g., the eaCas9 molecule comprises a mutation at H840, e.g., H840A. In another embodiment, the eaCas9 molecule is an N-terminal RuvC-like domain nickase, e.g., the eaCas9 molecule comprises a mutation at H863, e.g., H863A.

A nucleic acid disclosed herein may comprise (a) a sequence that encodes a gRNA molecule comprising a targeting domain that is complementary with a target domain in the CEP290 gene as disclosed herein; and (b) a sequence that encodes a Cas9 molecule.

A nucleic acid disclosed herein may comprise (a) a sequence that encodes a gRNA molecule comprising a targeting domain that is complementary with a target domain in the CEP290 gene as disclosed herein; (b) a sequence that encodes a Cas9 molecule; and further comprises (c)(i) a sequence that encodes a second gRNA molecule described herein having a targeting domain that is complementary to a second target domain of the CEP290 gene, and optionally, (ii) a sequence that encodes a third gRNA molecule described herein having a targeting domain that is complementary to a third target domain of the CEP290 gene; and optionally, (iii) a sequence that encodes a fourth gRNA molecule described herein having a targeting domain that is complementary to a fourth target domain of the CEP290 gene.

In an embodiment, a nucleic acid encodes a second gRNA molecule comprising a targeting domain configured to provide a cleavage event, e.g., a double strand break or a single strand break, sufficiently close to a LCA10 target position in the CEP290 gene to allow alteration, e.g., alteration associated with NHEJ, of the LCA10 target position, either alone or in combination with the break positioned by said first gRNA molecule.

In an embodiment, a nucleic acid encodes a third gRNA molecule comprising a targeting domain configured to provide a cleavage event, e.g., a double strand break or a single strand break, sufficiently close to a LCA10 target position in the CEP290 gene to allow alteration, e.g., alteration associated with NHEJ, either alone or in combination with the break positioned by the first and/or second gRNA molecule.

In an embodiment, a nucleic acid encodes a fourth gRNA molecule comprising a targeting domain configured to provide a cleavage event, e.g., a double strand break or a single strand break, sufficiently close to a LCA10 target position in the CEP290 gene to allow alteration, e.g., alteration associated with NHEJ, either alone or in combination with the break positioned by the first gRNA molecule, the second gRNA molecule and/or the third gRNA molecule.

In an embodiment, a nucleic acid encodes a second gRNA molecule comprising a targeting domain configured to provide a cleavage event, e.g., a double strand break or a single strand break, in combination with the break position by said first gRNA molecule, sufficiently close to a LCA10 target position in the CEP290 gene to allow alteration, e.g., alteration associated with NHEJ, of the a LCA10 target position in the CEP290 gene, either alone or in combination with the break positioned by said first gRNA molecule.

In an embodiment, a nucleic acid encodes a third gRNA molecule comprising a targeting domain configured to provide a cleavage event, e.g., a double strand break or a single strand break, in combination with the break position by said first and/or second gRNA molecule sufficiently close to a LCA10 target position in the CEP290 gene to allow alteration, e.g., alteration associated with NHEJ, either alone or in combination with the break positioned by the first and/or second gRNA molecule.

In an embodiment, a nucleic acid encodes a fourth gRNA molecule comprising a targeting domain configured to provide a cleavage event, e.g., a double strand break or a single strand break, in combination with the break positioned by the first gRNA molecule, the second gRNA molecule and/or the third gRNA molecule, sufficiently close to a LCA10 target position in the CEP290 gene to allow alteration, e.g., alteration associated with NHEJ, either alone or in combination with the break positioned by the first gRNA molecule, the second gRNA molecule and/or the third gRNA molecule.

In an embodiment, the nucleic acid encodes a second gRNA molecule. The second gRNA is selected to target the LCA10 target position. Optionally, the nucleic acid may encode a third gRNA, and further optionally, the nucleic acid may encode a fourth gRNA molecule.

In an embodiment, the nucleic acid encodes a second gRNA molecule comprising a targeting domain comprising a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from one of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. In an embodiment, the nucleic acid encodes a second gRNA molecule comprising a targeting domain selected from those in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. In an embodiment, when a third or fourth gRNA molecule are present, the third and fourth gRNA molecules may independently comprise a targeting domain comprising a sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from one of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. In a further embodiment, when a third or fourth gRNA molecule are present, the third and fourth gRNA molecules may independently comprise a targeting domain selected from those in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11.

In an embodiment, the nucleic acid encodes a second gRNA which is a modular gRNA, e.g., wherein one or more nucleic acid molecules encode a modular gRNA. In other embodiments, the nucleic acid encoding a second gRNA is a chimeric gRNA. In other embodiments, when a nucleic acid encodes a third or fourth gRNA, the third and fourth gRNA may be a modular gRNA or a chimeric gRNA. When multiple gRNAs are used, any combination of modular or chimeric gRNAs may be used.

A nucleic acid may encode a second, a third, and/or a fourth gRNA, each independently, comprising a targeting domain comprising 16 nucleotides or more in length. In an embodiment, the nucleic acid encodes a second gRNA comprising a targeting domain that is 16 nucleotides in length. In other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 17 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 18 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 19 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 20 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 21 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 22 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 23 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 24 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 25 nucleotides in length. In still other embodiments, the nucleic acid encodes a second gRNA comprising a targeting domain that is 26 nucleotides in length.

In an embodiment, the targeting domain comprises 16 nucleotides.

In an embodiment, the targeting domain comprises 17 nucleotides.

In an embodiment, the targeting domain comprises 18 nucleotides.

In an embodiment, the targeting domain comprises 19 nucleotides.

In an embodiment, the targeting domain comprises 20 nucleotides.

In an embodiment, the targeting domain comprises 21 nucleotides.

In an embodiment, the targeting domain comprises 22 nucleotides.

In an embodiment, the targeting domain comprises 23 nucleotides.

In an embodiment, the targeting domain comprises 24 nucleotides.

In an embodiment, the targeting domain comprises 25 nucleotides.

In an embodiment, the targeting domain comprises 26 nucleotides.

In an embodiment, a nucleic acid encodes a second, a third, and/or a fourth gRNA, each independently, comprising from 5′ to 3′: a targeting domain (comprising a “core domain”, and optionally a “secondary domain”); a first complementarity domain; a linking domain; a second complementarity domain; a proximal domain; and a tail domain. In some embodiments, the proximal domain and tail domain are taken together as a single domain.

In an embodiment, a nucleic acid encodes a second, a third, and/or a fourth gRNA, each independently, comprising a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 20 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, a nucleic acid encodes a second, a third, and/or a fourth gRNA, each independently, comprising a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 30 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, a nucleic acid encodes a second, a third, and/or a fourth gRNA, each independently, comprising a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 30 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, a nucleic acid encodes a second, a third, and/or a fourth gRNA, each independently, comprising a linking domain of no more than 25 nucleotides in length; a proximal and tail domain, that taken together, are at least 40 nucleotides in length; and a targeting domain of equal to or greater than 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In some embodiments, when the CEP290 gene is altered, e.g., by NHEJ, the nucleic acid encodes (a) a sequence that encodes a gRNA molecule comprising a targeting domain that is complementary with a target domain in the CEP290 gene as disclosed herein; (b) a sequence that encodes a Cas9 molecule; optionally, (c)(i) a sequence that encodes a second gRNA molecule described herein having a targeting domain that is complementary to a second target domain of the CEP290 gene, and further optionally, (ii) a sequence that encodes a third gRNA molecule described herein having a targeting domain that is complementary to a third target domain of the CEP290 gene; and still further optionally, (iii) a sequence that encodes a fourth gRNA molecule described herein having a targeting domain that is complementary to a fourth target domain of the CEP290 gene.

As described above, a nucleic acid may comprise (a) a sequence encoding a gRNA molecule comprising a targeting domain that is complementary with a target domain in the CEP290, and (b) a sequence encoding a Cas9 molecule. In some embodiments, (a) and (b) are present on the same nucleic acid molecule, e.g., the same vector, e.g., the same viral vector, e.g., the same adeno-associated virus (AAV) vector. In an embodiment, the nucleic acid molecule is an AAV vector, e.g., an AAV vector described herein. Exemplary AAV vectors that may be used in any of the described compositions and methods include an AAV1 vector, a modified AAV1 vector, an AAV2 vector, a modified AAV2 vector, an AAV3 vector, a modified AAV3 vector, an AAV4 vector, a modified AAV4 vector, an AAVS vector, a modified AAVS vector, an AAV6 vector, a modified AAV6 vector, an AAV7 vector, a modified AAV7 vector, an AAV8 vector, an AAVS vector, an AAV.rh10 vector, a modified AAV.rh10 vector, an AAV.rh32/33 vector, a modified AAV.rh32/33 vector, an AAV.rh43 vector, a modified AAV.rh43 vector, an AAV.rh64R1 vector, and a modified AAV.rh64R1 vector.

In other embodiments, (a) is present on a first nucleic acid molecule, e.g. a first vector, e.g., a first viral vector, e.g., a first AAV vector; and (b) is present on a second nucleic acid molecule, e.g., a second vector, e.g., a second vector, e.g., a second AAV vector. The first and second nucleic acid molecules may be AAV vectors, e.g., the AAV vectors described herein.

In other embodiments, the nucleic acid may further comprise (c)(i) a sequence that encodes a second gRNA molecule as described herein. In some embodiments, the nucleic acid comprises (a), (b) and (c)(i). Each of (a) and (c)(i) may be present on the same nucleic acid molecule, e.g., the same vector, e.g., the same viral vector, e.g., the same adeno-associated virus (AAV) vector. In an embodiment, the nucleic acid molecule is an AAV vector, e.g., an AAV vectors described herein.

In other embodiments, (a) and (c)(i) are on different vectors. For example, (a) may be present on a first nucleic acid molecule, e.g. a first vector, e.g., a first viral vector, e.g., a first AAV vector; and (c)(i) may be present on a second nucleic acid molecule, e.g., a second vector, e.g., a second vector, e.g., a second AAV vector. In an embodiment, the first and second nucleic acid molecules are AAV vectors, e.g., the AAV vectors described herein.

In another embodiment, each of (a), (b), and (c)(i) are present on the same nucleic acid molecule, e.g., the same vector, e.g., the same viral vector, e.g., an AAV vector. In an embodiment, the nucleic acid molecule is an AAV vector. In an alternate embodiment, one of (a), (b), and (c)(i) is encoded on a first nucleic acid molecule, e.g., a first vector, e.g., a first viral vector, e.g., a first AAV vector; and a second and third of (a), (b), and (c)(i) is encoded on a second nucleic acid molecule, e.g., a second vector, e.g., a second vector, e.g., a second AAV vector. The first and second nucleic acid molecule may be AAV vectors, e.g., the AAV vectors described herein.

In an embodiment, (a) is present on a first nucleic acid molecule, e.g., a first vector, e.g., a first viral vector, a first AAV vector; and (b) and (c)(i) are present on a second nucleic acid molecule, e.g., a second vector, e.g., a second vector, e.g., a second AAV vector. The first and second nucleic acid molecule may be AAV vectors, e.g., the AAV vectors described herein.

In other embodiments, (b) is present on a first nucleic acid molecule, e.g., a first vector, e.g., a first viral vector, e.g., a first AAV vector; and (a) and (c)(i) are present on a second nucleic acid molecule, e.g., a second vector, e.g., a second vector, e.g., a second AAV vector. The first and second nucleic acid molecule may be AAV vectors, e.g., the AAV vectors described herein.

In other embodiments, (c)(i) is present on a first nucleic acid molecule, e.g., a first vector, e.g., a first viral vector, e.g., a first AAV vector; and (b) and (a) are present on a second nucleic acid molecule, e.g., a second vector, e.g., a second vector, e.g., a second AAV vector. The first and second nucleic acid molecule may be AAV vectors, e.g., the AAV vectors described herein.

In another embodiment, each of (a), (b) and (c)(i) are present on different nucleic acid molecules, e.g., different vectors, e.g., different viral vectors, e.g., different AAV vector. For example, (a) may be on a first nucleic acid molecule, (b) on a second nucleic acid molecule, and (c)(i) on a third nucleic acid molecule. The first, second and third nucleic acid molecule may be AAV vectors, e.g., the AAV vectors described herein.

In another embodiment, when a third and/or fourth gRNA molecule are present, each of (a), (b), (c)(i), (c) (ii) and (c)(iii) may be present on the same nucleic acid molecule, e.g., the same vector, e.g., the same viral vector, e.g., an AAV vector. In an embodiment, the nucleic acid molecule is an AAV vector, e.g., an AAV vector. In an alternate embodiment, each of (a), (b), (c)(i), (c)(ii) and (c)(iii) may be present on the different nucleic acid molecules, e.g., different vectors, e.g., the different viral vectors, e.g., different AAV vectors. In further embodiments, each of (a), (b), (c)(i), (c) (ii) and (c)(iii) may be present on more than one nucleic acid molecule, but fewer than five nucleic acid molecules, e.g., AAV vectors, e.g., the AAV vectors described herein.

The nucleic acids described herein may comprise a promoter operably linked to the sequence that encodes the gRNA molecule of (a), e.g., a promoter described herein, e.g., a promoter described in Table 20. The nucleic acid may further comprise a second promoter operably linked to the sequence that encodes the second, third and/or fourth gRNA molecule of (c), e.g., a promoter described herein. The promoter and second promoter differ from one another. In some embodiments, the promoter and second promoter are the same.

The nucleic acids described herein may further comprise a promoter operably linked to the sequence that encodes the Cas9 molecule of (b), e.g., a promoter described herein, e.g., a promoter described in Table 20.

In another aspect, disclosed herein is a composition comprising (a) a gRNA molecule comprising a targeting domain that is complementary with a target domain in the CEP290 gene, as described herein. The composition of (a) may further comprise (b) a Cas9 molecule, e.g., a Cas9 molecule as described herein. A composition of (a) and (b) may further comprise (c) a second, third and/or fourth gRNA molecule, e.g., a second, third and/or fourth gRNA molecule described herein.

In another aspect, methods and compositions discussed herein, provide for treating or delaying the onset or progression of LCA10 by altering the LCA10 target position in the CEP290 gene.

In another aspect, disclosed herein is a method of altering a cell, e.g., altering the structure, e.g., altering the sequence, of a target nucleic acid of a cell, comprising contacting said cell with: (a) a gRNA that targets the CEP290 gene, e.g., a gRNA as described herein; (b) a Cas9 molecule, e.g., a Cas9 molecule as described herein; and optionally, (c) a second, third and/or fourth gRNA that targets CEP290 gene, e.g., a gRNA as described herein.

In some embodiments, the method comprises contacting said cell with (a) and (b).

In some embodiments, the method comprises contacting said cell with (a), (b), and (c).

The gRNA of (a) may be selected from any of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, or a gRNA that differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from any of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. The gRNA of (c) may be selected from any of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, or a gRNA that differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from any of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11.

In some embodiments, the method comprises contacting a cell from a subject suffering from or likely to develop LCA10. The cell may be from a subject having a mutation at a LCA10 target position.

In some embodiments, the cell being contacted in the disclosed method is a photoreceptor cell. The contacting may be performed ex vivo and the contacted cell may be returned to the subject's body after the contacting step. In other embodiments, the contacting step may be performed in vivo.

In some embodiments, the method of altering a cell as described herein comprises acquiring knowledge of the presence of a LCA10 target position in said cell, prior to the contacting step. Acquiring knowledge of the presence of a LCA10 target position in the cell may be by sequencing the CEP290 gene, or a portion of the CEP290 gene.

In some embodiments, the contacting step of the method comprises contacting the cell with a nucleic acid, e.g., a vector, e.g., an AAV vector, e.g., an AAV vector described herein, that expresses at least one of (a), (b), and (c). In some embodiments, the contacting step of the method comprises contacting the cell with a nucleic acid, e.g., a vector, e.g., an AAV vector, that expresses each of (a), (b), and (c). In another embodiment, the contacting step of the method comprises delivering to the cell a Cas9 molecule of (b) and a nucleic acid which encodes a gRNA (a) and optionally, a second gRNA (c)(i) (and further optionally, a third gRNA (c)(iv) and/or fourth gRNA (c)(iii)).

In an embodiment, contacting comprises contacting the cell with a nucleic acid, e.g., a vector, e.g., an AAV vector, e.g., an AAV1 vector, a modified AAV1 vector, an AAV2 vector, a modified AAV2 vector, an AAV3 vector, a modified AAV3 vector, an AAV4 vector, a modified AAV4 vector, an AAVS vector, a modified AAVS vector, an AAV6 vector, a modified AAV6 vector, an AAV7 vector, a modified AAV7 vector, an AAV8 vector, an AAVS vector, an AAV.rh10 vector, a modified AAV.rh10 vector, an AAV.rh32/33 vector, a modified AAV.rh32/33 vector, an AAV.rh43vector, a modified AAV.rh43vector, an AAV.rh64R1vector, and a modified AAV.rh64R1vector, e.g., an AAV vector described herein.

In an embodiment, contacting comprises delivering to said cell said Cas9 molecule of (b), as a protein or an mRNA, and a nucleic acid which encodes and (a) and optionally (c).

In an embodiment, contacting comprises delivering to said cell said Cas9 molecule of (b), as a protein or an mRNA, said gRNA of (a), as an RNA, and optionally said second gRNA of (c), as an RNA.

In an embodiment, contacting comprises delivering to said cell said gRNA of (a) as an RNA, optionally said second gRNA of (c) as an RNA, and a nucleic acid that encodes the Cas9 molecule of (b).

In another aspect, disclosed herein is a method of treating, or preventing a subject suffering from developing, LCA10, e.g., by altering the structure, e.g., sequence, of a target nucleic acid of the subject, comprising contacting the subject (or a cell from the subject) with:

(a) a gRNA that targets the CEP290 gene, e.g., a gRNA disclosed herein;

(b) a Cas9 molecule, e.g., a Cas9 molecule disclosed herein; and

optionally, (c)(i) a second gRNA that targets the CEP290 gene, e.g., a second gRNA disclosed herein, and

further optionally, (c)(ii) a third gRNA, and still further optionally, (c)(iii) a fourth gRNA that target the CEP290, e.g., a third and fourth gRNA disclosed herein.

In some embodiments, contacting comprises contacting with (a) and (b).

In some embodiments, contacting comprises contacting with (a), (b), and (c)(i).

In some embodiments, contacting comprises contacting with (a), (b), (c)(i) and (c)(ii).

In some embodiments, contacting comprises contacting with (a), (b), (c)(i), (c)(ii) and (c)(iii).

The gRNA of (a) or (c) (e.g., (c)(i), (c)(ii), or (c)(iii)) may be independently selected from any of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, or a gRNA that differs by no more than 1, 2, 3, 4, or 5 nucleotides from, a targeting domain sequence from any of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11.

In an embodiment, said subject is suffering from, or likely to develop LCA10. In an embodiment, said subject has a mutation at a LCA10 target position.

In an embodiment, the method comprises acquiring knowledge of the presence of a mutation at a LCA10 target position in said subject.

In an embodiment, the method comprises acquiring knowledge of the presence of a mutation a LCA10 target position in said subject by sequencing the CEP290 gene or a portion of the CEP290 gene.

In an embodiment, the method comprises altering the LCA10 target position in the CEP290 gene.

In an embodiment, a cell of said subject is contacted ex vivo with (a), (b) and optionally (c). In an embodiment, said cell is returned to the subject's body.

In an embodiment, the method comprises introducing a cell into said subject's body, wherein said cell subject was contacted ex vivo with (a), (b) and optionally (c).

In an embodiment, the method comprises said contacting is performed in vivo. In an embodiment, the method comprises sub-retinal delivery. In an embodiment, contacting comprises sub-retinal injection. In an embodiment, contacting comprises intra-vitreal injection.

In an embodiment, contacting comprises contacting the subject with a nucleic acid, e.g., a vector, e.g., an AAV vector described herein, e.g., a nucleic acid that encodes at least one of (a), (b), and optionally (c).

In an embodiment, contacting comprises delivering to said subject said Cas9 molecule of (b), as a protein or mRNA, and a nucleic acid which encodes and (a) and optionally (c).

In an embodiment, contacting comprises delivering to said subject said Cas9 molecule of (b), as a protein or mRNA, said gRNA of (a), as an RNA, and optionally said second gRNA of (c), as an RNA.

In an embodiment, contacting comprises delivering to said subject said gRNA of (a), as an RNA, optionally said second gRNA of (c), as an RNA, and a nucleic acid that encodes the Cas9 molecule of (b).

In another aspect, disclosed herein is a reaction mixture comprising a gRNA, a nucleic acid, or a composition described herein, and a cell, e.g., a cell from a subject having, or likely to develop LCA10, or a subject having a mutation at a LCA10 target position.

In another aspect, disclosed herein is a kit comprising, (a) a gRNA molecule described herein, or a nucleic acid that encodes said gRNA, and one or more of the following:

(b) a Cas9 molecule, e.g., a Cas9 molecule described herein, or a nucleic acid or mRNA that encodes the Cas9;

(c)(i) a second gRNA molecule, e.g., a second gRNA molecule described herein or a nucleic acid that encodes (c)(i);

(c)(ii) a third gRNA molecule, e.g., a second gRNA molecule described herein or a nucleic acid that encodes (c)(ii); or

(c)(iii) a fourth gRNA molecule, e.g., a second gRNA molecule described herein or a nucleic acid that encodes (c)(iii).

In an embodiment, the kit comprises nucleic acid, e.g., an AAV vector, e.g., an AAV vector described herein, that encodes one or more of (a), (b), (c)(i), (c)(ii), and (c)(iii). In an embodiment, the kit further comprises a governing gRNA molecule, or a nucleic acid that encodes a governing gRNA molecule.

In yet another aspect, disclosed herein is a gRNA molecule, e.g., a gRNA molecule described herein, for use in treating LCA10 in a subject, e.g., in accordance with a method of treating LCA10 as described herein.

In an embodiment, the gRNA molecule in used in combination with a Cas9 molecule, e.g., a Cas9 molecule described herein. Additionally or alternatively, in an embodiment, the gRNA molecule is used in combination with a second, third and/or fourth gRNA molecule, e.g., a second, third and/or fourth gRNA molecule described herein.

In still another aspect, disclosed herein is use of a gRNA molecule, e.g., a gRNA molecule described herein, in the manufacture of a medicament for treating LCA10 in a subject, e.g., in accordance with a method of treating LCA10 as described herein.

In an embodiment, the medicament comprises a Cas9 molecule, e.g., a Cas9 molecule described herein. Additionally or alternatively, in an embodiment, the medicament comprises a second, third and/or fourth gRNA molecule, e.g., a second, third and/or fourth gRNA molecule described herein.

In one aspect, disclosed herein is a recombinant adenovirus-associated virus (AAV) genome comprising the following components:

wherein the left ITR component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, any of the left ITR nucleotide sequences disclosed in Table 25, or any of the nucleotide sequences of SEQ ID NOs: 407-415;

wherein the spacer 1 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length, e.g., SEQ ID NO: 416;

wherein the PIII promoter component comprises, or consists of, an RNA polymerase III promoter sequence;

wherein the gRNA component comprises a targeting domain and a scaffold domain,

-   -   wherein the targeting domain is 16-26 nucleotides in length, and         comprises, or consists of, a targeting domain sequence disclosed         herein, e.g., in any of Tables 2A-2D, Tables 3A-3C, Tables         4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D,         Tables 9A-9E, Tables 10A-10B, or Table 11; and     -   wherein the scaffold domain (also referred to as a tracr domain         in FIGS. 20A-25F) comprises, or consists of, a nucleotide         sequence that is the same as, differs by no more than 1, 2, 3,         4, or 5 nucleotides from, or has at least has at least 90%, 92%,         94%, 96%, 98%, or 99% homology with, a nucleotide sequence of         SEQ ID NO: 418;

wherein the spacer 2 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length e.g., SEQ ID NO: 419;

wherein the PII promoter component comprises, or consists of, a polymerase II promoter sequence, e.g., a constitutive or tissue specific promoter, e.g., a promoter disclosed in Table 20;

wherein the N-ter NLS component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, or 5 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 420 or a nucleotide sequence that encodes the amino acid sequence of SEQ ID NO: 434;

wherein the Cas9 component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 421 or a nucleotide sequence that encodes the amino acid sequence of SEQ ID NO: 26;

wherein the C-ter NLS component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, or 5 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 422 or a nucleotide sequence that encodes the amino acid sequence of SEQ ID NO: 434;

wherein the poly(A) signal component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, any of the nucleotide sequences disclosed in Table 27, or any of the nucleotide sequences of SEQ ID NOs: 424, 455 or 456;

wherein the spacer 3 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length, e.g., SEQ ID NO: 425; and

wherein the right ITR component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, any of the right ITR nucleotide sequences disclosed in Table 25, or any of the nucleotide sequences of SEQ ID NOs: 436-444.

In an embodiment, the left ITR component comprises, or consists of, a nucleotide sequence that is the same as any of the nucleotide sequences of SEQ ID NOs: 407-415.

In an embodiment, the spacer 1 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 416.

In an embodiment, the PIII promoter component is a U6 promoter component.

In an embodiment, the U6 promoter component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 417;

In an embodiment, the U6 promoter component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 417.

In an embodiment, the PIII promoter component is an H1 promoter component that comprises an H1 promoter sequence.

In an embodiment, the PIII promoter component is a tRNA promoter component that comprises a tRNA promoter sequence.

In an embodiment, the targeting domain comprises, or consists of, a nucleotide sequence that is the same as a nucleotide sequence selected from Table 11.

In an embodiment, the gRNA scaffold domain comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 418.

In an embodiment, the spacer 2 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 419;

In an embodiment, the PII promoter component is a CMV promoter component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 401. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 401.

In an embodiment, the PII promoter component is an EFS promoter component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 402. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 402.

In an embodiment, the PII promoter component is a GRK1 promoter (e.g., a human GRK1 promoter) component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 403. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 403.

In an embodiment, the PII promoter component is a CRX promoter (e.g., a human CRX promoter) component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 404. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 404.

In an embodiment, the PII promoter component is an NRL promoter (e.g., a human NRL promoter) component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 405. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 405.

In an embodiment, the PII promoter component is an RCVRN promoter (e.g., a human RCVRN promoter) component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 406. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 406.

In an embodiment, the N-ter NLS component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 420 or a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 434.

In an embodiment, the Cas9 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 421 or a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 26.

In an embodiment, the C-ter NLS component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 422 or a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 434.

In an embodiment, the poly(A) signal component comprises, or consists of, a nucleotide sequence that is the same as any of the nucleotide sequences disclosed in Table 27, or any of the nucleotide sequences of SEQ ID NOs: 424, 455 or 456. In an embodiment, the poly(A) signal component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 424.

In an embodiment, the spacer 3 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 425.

In an embodiment, the right ITR component comprises, or consists of, a nucleotide sequence that is the same as any of the nucleotide sequences of SEQ ID NOs: 436-444.

In an embodiment, the recombinant AAV genome further comprises a second gRNA component comprising a targeting domain and a scaffold domain,

wherein the targeting domain consists of a targeting domain sequence disclosed herein, in any of Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11; and

wherein the scaffold domain (also referred to as a tracr domain in FIGS. 20A-25F) comprises, or consists of, a nucleotide sequence that is the same as, or differs by no more than 1, 2, 3, 4, or 5 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 418.

In an embodiment, the targeting domain of the second gRNA component comprises, or consists of, a nucleotide sequence that is the same as a nucleotide sequence selected from Table 11. In an embodiment, the second gRNA component is between the first gRNA component and the spacer 2 component.

In an embodiment, the second gRNA component has the same nucleotide sequence as the first gRNA component. In another embodiment, the second gRNA component has a nucleotide sequence that is different from the second gRNA component.

In an embodiment, the recombinant AAV genome further comprises a second PIII promoter component that comprises, or consists of, an RNA polymerase III promoter sequence;

In an embodiment, the recombinant AAV genome further comprises a second PIII promoter component (e.g., a second U6 promoter component) between the first gRNA component and the second gRNA component.

In an embodiment, the second PIII promoter component (e.g., the second U6 promoter component) has the same nucleotide sequence as the first PIII promoter component (e.g., the first U6 promoter component). In another embodiment, the second PIII promoter component (e.g., the second U6 promoter component) has a nucleotide sequence that is different from the first PIII promoter component (e.g. the first U6 promoter component).

In an embodiment, the PIII promoter component is an H1 promoter component that comprises an H1 promoter sequence.

In an embodiment, the PIII promoter component is a tRNA promoter component that comprises a tRNA promoter sequence.

In an embodiment, the recombinant AAV genome further comprises a spacer 4 component between the first gRNA component and the second PIII promoter component (e.g., the second U6 promoter component). In an embodiment, the spacer 4 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length, e.g., SEQ ID NO: 427. In an embodiment, the spacer 4 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 427.

In an embodiment, the recombinant AAV genome comprises the following components:

-   

In an embodiment, the recombinant AAV genome further comprises an affinity tag component (e.g., 3xFLAG component), wherein the affinity tag component (e.g., 3xFLAG component) comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, or 5 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotides sequence of SEQ ID NO: 423, or a nucleotide sequence encoding any of the amino acid sequences disclosed in Table 26 or any of the amino acid sequences of SEQ ID NOs: 426 or 451-454.

In an embodiment, the affinity tag component (e.g., 3xFLAG component) is between the C-ter NLS component and the poly(A) signal component. In an embodiment, the an affinity tag component (e.g., 3xFLAG component) comprises, or consists of, a nucleotide sequence that is the same as, the nucleotides sequence of SEQ ID NO: 423, or a nucleotide sequence encoding any of the amino acid sequences of SEQ ID NOs: 426 or 451-454.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 401, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 402, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 403, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 404, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 405, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 406, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome further comprises SEQ ID NOs: 416, 419, and 425, and, optionally, SEQ ID NO 427.

In an embodiment, the recombinant AAV genome further comprises the nucleotide sequence of SEQ ID NO: 423.

In an embodiment, the recombinant AAV genome comprises or consists of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all) of the component sequences shown in FIGS. 19A-19G, 20A-20F, 21A-21F, 22A-22F, 23A-23F, or 24A-24F, Tables 20 or 25-27, or any of the nucleotide sequences of SEQ ID NOs: 428-433 or 436-444.

In another aspect, disclosed herein is a recombinant adenovirus-associated virus (AAV) genome comprising the following components:

-   

wherein the left ITR component comprises, or consists of, a nucleotide sequence that is the same as, or differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, any of the left ITR nucleotide sequences disclosed in Table 25, or any of the nucleotide sequences of SEQ ID NOs: 407-415;

wherein the spacer 1 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length, e.g., SEQ ID NO: 416;

wherein the first PIII promoter component (e.g., a first U6 promoter component) comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 417;

wherein the first gRNA component comprises a targeting domain and a scaffold domain,

-   -   wherein the targeting domain is 16-26 nucleotides in length, and         comprises, or consists of, a targeting domain sequence disclosed         herein, e.g., in any of Tables 2A-2D, Tables 3A-3C, Tables         4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D,         Tables 9A-9E, Tables 10A-10B, or Table 11; and     -   wherein the scaffold domain (also referred to herein as a tracr         domain in FIGS. 19A-24F) comprises, or consists of, a nucleotide         sequence that is the same as, or differs by no more than 1, 2,         3, 4, or 5 nucleotides from, or has at least has at least 90%,         92%, 94%, 96%, 98%, or 99% homology with, the nucleotide         sequence of SEQ ID NO: 418;

wherein the spacer 4 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length, e.g., SEQ ID NO: 427.

wherein the second gRNA component comprises a targeting domain and a scaffold domain,

-   -   wherein the targeting domain of the second gRNA component is         16-26 nucleotides in length and comprises, or consists of, a         targeting domain sequence disclosed herein, e.g., in any of         Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables         6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B,         or Table 11; and     -   wherein the scaffold domain (also referred to as a tracr domain         in FIGS. 19A-24F) of the second gRNA component comprises, or         consists of, a nucleotide sequence that is the same as, or         differs by no more than 1, 2, 3, 4, or 5 nucleotides from, or         has at least has at least 90%, 92%, 94%, 96%, 98%, or 99%         homology with, the nucleotide sequence of SEQ ID NO: 418.

wherein the spacer 2 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length e.g., SEQ ID NO: 419;

wherein the PII promoter component comprises, or consists of, a polymerase II promoter sequence, e.g., a constitutive or tissue specific promoter, e.g., a promoter disclosed in Table 20;

wherein the N-ter NLS component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, or 5 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 420 or a nucleotide sequence that encodes the amino acid sequence of SEQ ID NO: 434;

wherein the Cas9 component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 421 or a nucleotide sequence that encodes the amino acid sequence of SEQ ID NO: 26;

wherein the C-ter NLS component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, or 5 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 422 or a nucleotide sequence that encodes the amino acid sequence of SEQ ID NO: 434;

wherein the poly(A) signal component comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, any of the nucleotide sequences disclosed in Table 27, or any of the nucleotide sequence of SEQ ID NO: 424, 455 or 456;

wherein the spacer 3 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length, e.g., SEQ ID NO: 425; and

wherein the right ITR component comprises, or consists of, a nucleotide sequence that is the same as, or differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, any of the right ITR nucleotide sequences disclosed in Table 25, or SEQ ID NOs: 436-444.

In an embodiment, the left ITR component comprises, or consists of, a nucleotide sequence that is the same as any of the nucleotide sequences of SEQ ID NOs: 407-415.

In an embodiment, the spacer 1 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 416.

In an embodiment, the first PIII promoter component (e.g., the first U6 promoter component) comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 417.

In an embodiment, the first PIII promoter is an H1 promoter component that comprises an H1 promoter sequence. In another embodiment, the first PIII promoter is a tRNA promoter component that comprises a tRNA promoter sequence.

In an embodiment, the targeting domain of the first gRNA component comprises, or consists of, a nucleotide sequence that is the same as a nucleotide sequence selected from Table 11.

In an embodiment, the gRNA scaffold domain of the first gRNA component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 418.

In an embodiment, the spacer 4 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 427.

In an embodiment, the second PIII promoter component (e.g., the first U6 promoter component) has the same nucleotide sequence as the first PIII promoter component (e.g., the first U6 promoter component). In another embodiment, the second PIII promoter component (e.g., the second U6 promoter component) has a nucleotide sequence that is different from the first PIII promoter component (e.g., the first U6 promoter component).

In an embodiment, the second PIII promoter is an H1 promoter component that comprises an H1 promoter sequence. In another embodiment, the second PIII promoter is a tRNA promoter component that comprises a tRNA promoter sequence.

In an embodiment, the targeting domain of the second gRNA component comprises, or consists of, a nucleotide sequence that is the same as a nucleotide sequence selected from Table 11.

In an embodiment, the second gRNA component has the same nucleotide sequence as the first gRNA component. In another embodiment, the second gRNA component has a nucleotide sequence that is different from the second gRNA component.

In an embodiment, the spacer 2 component comprises, or consists of, a nucleotide sequence having 0 to 150 nucleotides in length e.g., SEQ ID NO: 419;

In an embodiment, the PII promoter component is a CMV promoter component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 401. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 401.

In an embodiment, the PII promoter component is an EFS promoter component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 402. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 402.

In an embodiment, the PII promoter component is a GRK1 promoter (e.g., a human GRK1 promoter) component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 403. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 403.

In an embodiment, the PII promoter component is a CRX promoter (e.g., a human CRX promoter) component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 404. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 404.

In an embodiment, the PII promoter component is an NRL promoter (e.g., a human NRL promoter) component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 405. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 405.

In an embodiment, the PII promoter component is an RCVRN promoter (e.g., a human RCVRN promoter) component, and comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 406. In an embodiment, the PII promoter comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 406.

In an embodiment, the N-ter NLS component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 420 or a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 434.

In an embodiment, the Cas9 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 421 or a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 26.

In an embodiment, the C-ter NLS component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 422 or a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 434.

In an embodiment, the poly(A) signal component comprises, or consists of, a nucleotide sequence that is the same as any of the nucleotide sequences disclosed in Table 27, or any of the nucleotide sequences of SEQ ID NOs: 424, 455 or 456. In an embodiment, the poly(A) signal component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 424.

In an embodiment, the spacer 3 component comprises, or consists of, a nucleotide sequence that is the same as the nucleotide sequence of SEQ ID NO: 425.

In an embodiment, the right ITR component comprises, or consists of, a nucleotide sequence that is the same as any of the nucleotide sequences disclosed in Table 25, or any of the nucleotide sequences of SEQ ID NOs: 436-444.

In an embodiment, the recombinant AAV genome further comprises an affinity tag component (e.g., a 3xFLAG component). In an embodiment, the affinity tag component (e.g., the 3xFLAG component) comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 1, 2, 3, 4, or 5 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with, the nucleotide sequence of SEQ ID NO: 423, or a nucleotide sequence encoding any of the amino acid sequences disclosed in Table 26 or any of the amino acid sequences of SEQ ID NO: 426 or 451-454.

In an embodiment, the affinity tag component (e.g., the 3xFLAG component) is between the C-ter NLS component and the poly(A) signal component. In an embodiment, the affinity tag component (e.g., the 3xFLAG component) comprises, or consists of, a nucleotide sequence that is the same as, the nucleotide sequence of SEQ ID NO: 423 or a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 426.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 401, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 402, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 403, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 404, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 405, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome comprises the nucleotide sequences of SEQ ID NOs: 408, 417, 418, 406, 420, 421, 422, 424, and 437.

In an embodiment, the recombinant AAV genome further comprises the nucleotide sequences of SEQ ID NO: 416, 419, 425, and 427.

In an embodiment, the recombinant AAV genome further comprises the nucleotide sequence of SEQ ID NO: 423.

In an embodiment, the recombinant AAV genome comprises any of the nucleotide sequences of SEQ ID NOs: 428-433.

In an embodiment, the recombinant AAV genome comprises, or consists of, a nucleotide sequence that is the same as, differs by no more than 100, 200, 300, 400, or 500 nucleotides from, or has at least has at least 90%, 92%, 94%, 96%, 98%, or 99% homology with any of the nucleotide sequences shown in FIGS. 19A-19G, 20A-20F, 21A-21F, 22A-22F, 23A-23F, or 24A-24F, or any of the nucleotide sequences of SEQ ID NOs: 428-433 or 436-444.

In an embodiment, the recombinant AAV genome comprises, or consists of, a nucleotide sequence that is the same as any of the nucleotide sequences shown in FIGS. 19A-19G, 20A-20F, 21A-21F, 22A-22F, 23A-23F, or 24A-24F, or any of the nucleotide sequences of SEQ ID NOs: 428-433 or 436-444.

In an embodiment, the recombinant AAV genome comprises or consists of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all) of the component sequences shown in FIGS. 19A-19G, 20A-20F, 21A-21F, 22A-22F, 23A-23F, or 24A-24F, or Tables 20 or 25-27, or any of the nucleotide sequences of SEQ ID NOs: 428-433 or 436-444.

Unless otherwise indicated, when components of a recombinant AAV genome are described herein, the order can be as provided, but other orders are included as well. In other words, in an embodiment, the order is as set out in the text, but in other embodiments, the order can be different.

It is understood that the recombinant AAV genomes disclosed herein can be single stranded or double stranded. Disclosed herein are also the reverse, complementary form of any of the recombinant AAV genomes disclosed herein, and the double stranded form thereof.

In another aspect, disclosed herein is a nucleic acid molecule (e.g., an expression vector) that comprises a recombinant AAV genome disclosed herein. In an embodiment, the nucleic acid molecule further comprises a nucleotide sequence that encodes an antibiotic resistant gene (e.g., an Amp resistant gene). In an embodiment, the nucleic acid molecule further comprises replication origin sequence (e.g., a ColE1 origin, an M13 origin, or both).

In another aspect, disclosed herein is a recombinant AAV viral particle comprising a recombinant AAV genome disclosed herein.

In an embodiment, the recombinant AAV viral particle has any of the serotype disclosed herein, e.g., in Table 25, or a combination thereof. In another embodiment, the recombinant AAV viral particle has a tissue specificity of retinal pigment epithelium cells, photoreceptors, horizontal cells, bipolar cells, amacrine cells, ganglion cells, or a combination thereof.

In another aspect, disclosed herein is a method of producing a recombinant AAV viral particle disclosed herein comprising providing a recombinant AAV genome disclosed herein and one or more capsid proteins under conditions that allow for assembly of an AAV viral particle.

In another aspect, disclosed herein is a method of altering a cell comprising contacting the cell with a recombinant AAV viral particle disclosed herein.

In another aspect, disclosed herein is a method of treating a subject having or likely to develop LCA10 comprising contacting the subject (or a cell from the subject) with a recombinant viral particle disclosed herein.

In another aspect, disclosed herein is a recombinant AAV viral particle comprising a recombinant AAV genome disclosed herein for use in treating LCA10 in a subject.

In another aspect, disclosed herein is use of a recombinant AAV viral particle comprising a recombinant AAV genome disclosed herein in the manufacture of a medicament for treating LCA10 in a subject.

The gRNA molecules and methods, as disclosed herein, can be used in combination with a governing gRNA molecule, comprising a targeting domain which is complementary to a target domain on a nucleic acid that encodes a component of the CRISPR/Cas system introduced into a cell or subject. In an embodiment, the governing gRNA molecule targets a nucleic acid that encodes a Cas9 molecule or a nucleic acid that encodes a target gene gRNA molecule. In an embodiment, the governing gRNA comprises a targeting domain that is complementary to a target domain in a sequence that encodes a Cas9 component, e.g., a Cas9 molecule or target gene gRNA molecule. In an embodiment, the target domain is designed with, or has, minimal homology to other nucleic acid sequences in the cell, e.g., to minimize off-target cleavage. For example, the targeting domain on the governing gRNA can be selected to reduce or minimize off-target effects. In an embodiment, a target domain for a governing gRNA can be disposed in the control or coding region of a Cas9 molecule or disposed between a control region and a transcribed region. In an embodiment, a target domain for a governing gRNA can be disposed in the control or coding region of a target gene gRNA molecule or disposed between a control region and a transcribed region for a target gene gRNA. While not wishing to be bound by theory, in an embodiment, it is believed that altering, e.g., inactivating, a nucleic acid that encodes a Cas9 molecule or a nucleic acid that encodes a target gene gRNA molecule can be effected by cleavage of the targeted nucleic acid sequence or by binding of a Cas9 molecule/governing gRNA molecule complex to the targeted nucleic acid sequence.

The compositions, reaction mixtures and kits, as disclosed herein, can also include a governing gRNA molecule, e.g., a governing gRNA molecule disclosed herein.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

Headings, including numeric and alphabetical headings and subheadings, are for organization and presentation and are not intended to be limiting.

Other features and advantages of the invention will be apparent from the detailed description, drawings, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1G are representations of several exemplary gRNAs.

FIG. 1A depicts a modular gRNA molecule derived in part (or modeled on a sequence in part) from Streptococcus pyogenes (S. pyogenes) as a duplexed structure (SEQ ID NOs: 42 and 43, respectively, in order of appearance);

FIG. 1B depicts a unimolecular (or chimeric) gRNA molecule derived in part from S. pyogenes as a duplexed structure (SEQ ID NO: 44);

FIG. 1C depicts a unimolecular gRNA molecule derived in part from S. pyogenes as a duplexed structure (SEQ ID NO: 45);

FIG. 1D depicts a unimolecular gRNA molecule derived in part from S. pyogenes as a duplexed structure (SEQ ID NO: 46);

FIG. 1E depicts a unimolecular gRNA molecule derived in part from S. pyogenes as a duplexed structure (SEQ ID NO: 47);

FIG. 1F depicts a modular gRNA molecule derived in part from Streptococcus thermophilus (S. thermophilus) as a duplexed structure (SEQ ID NOs: 48 and 49, respectively, in order of appearance);

FIG. 1G depicts an alignment of modular gRNA molecules of S. pyogenes (SEQ ID NOs: 42 and 52) and S. thermophilus (SEQ ID NOs: 48 and 49).

FIGS. 2A-2G depict an alignment of Cas9 sequences from Chylinski 2013. The N-terminal RuvC-like domain is boxed and indicated with a “Y”. The other two RuvC-like domains are boxed and indicated with a “B”. The HNH-like domain is boxed and indicated by a “G”. Sm: S. mutans (SEQ ID NO: 1); Sp: S. pyogenes (SEQ ID NO: 2); St: S. thermophilus (SEQ ID NO: 3); Li: L. innocua (SEQ ID NO: 4). Motif: this is a motif based on the four sequences: residues conserved in all four sequences are indicated by single letter amino acid abbreviation; “*” indicates any amino acid found in the corresponding position of any of the four sequences; and “-” indicates any amino acid, e.g., any of the 20 naturally occurring amino acids (SEQ ID NO: 2804).

FIGS. 3A-3B show an alignment of the N-terminal RuvC-like domain from the Cas9 molecules disclosed in Chylinski 2013 (SEQ ID NOs: 54, 56, and 58-103, respectively, in order of appearance). The last line of FIG. 3B identifies 4 highly conserved residues.

FIGS. 4A-4B show an alignment of the N-terminal RuvC-like domain from the Cas9 molecules disclosed in Chylinski 2013 with sequence outliers removed. The last line of FIG. 4B identifies 3 highly conserved residues.

FIGS. 5A-5C show an alignment of the HNH-like domain from the Cas9 molecules disclosed in Chylinski 2013 (SEQ ID NOs: 178-252, respectively, in order of appearance). The last line of FIG. 5C identifies conserved residues.

FIGS. 6A-6B show an alignment of the HNH-like domain from the Cas9 molecules disclosed in Chylinski 2013 with sequence outliers removed. The last line of FIG. 6B identifies 3 highly conserved residues.

FIGS. 7A-7B depict an alignment of Cas9 sequences from S. pyogenes and Neisseria meningitidis (N. meningitidis). The N-terminal RuvC-like domain is boxed and indicated with a “Y”. The other two RuvC-like domains are boxed and indicated with a “B”. The HNH-like domain is boxed and indicated with a “G”. Sp: S. pyogenes; Nm: N. meningitidis. Motif: this is a motif based on the two sequences: residues conserved in both sequences are indicated by a single amino acid designation; “*” indicates any amino acid found in the corresponding position of any of the two sequences; “-” indicates any amino acid, e.g., any of the 20 naturally occurring amino acids, and “-” indicates any amino acid, e.g., any of the 20 naturally occurring amino acids, or absent.

FIG. 8 shows a nucleic acid sequence encoding Cas9 of N. meningitidis (SEQ ID NO: 303). Sequence indicated by an “R” is an SV40 NLS; sequence indicated as “G” is an HA tag; and sequence indicated by an “O” is a synthetic NLS sequence; the remaining (unmarked) sequence is the open reading frame (ORF).

FIGS. 9A-9B are schematic representations of the domain organization of S. pyogenes Cas 9. FIG. 9A shows the organization of the Cas9 domains, including amino acid positions, in reference to the two lobes of Cas9 (recognition (REC) and nuclease (NUC) lobes). FIG. 9B shows the percent homology of each domain across 83 Cas9 orthologs.)

FIG. 10 shows the nucleotide locations of the Alu repeats, cryptic exon and point mutation, c.2991+1655 A to G in the human CEP290 locus. “X” indicates the cryptic exon. The blue triangle indicates the LCA target position c.2991+1655A to G.

FIG. 11A-11B show the rates of indels induced by various gRNAs at the CEP290 locus. FIG. 11A shows gene editing (% indels) as assessed by sequencing for S. pyogenes and S. aureus gRNAs when co-expressed with Cas9 in patient-derived IVS26 primary fibroblasts. FIG. 11B shows gene editing (% indels) as assessed by sequencing for S. aureus gRNAs when co-expressed with Cas9 in HEK293 cells.

FIGS. 12A-12B show changes in expression of the wild-type and mutant (including cryptic exon) alleles of CEP290 in cells transfected with Cas9 and the indicated gRNA pairs. Total RNA was isolated from modified cells and qRT-PCR with Taqman primer-probe sets was used to quantify expression. Expression is normalized to the Beta-Actin housekeeping gene and each sample is normalized to the GFP control sample (cells transfected with only GFP). Error bars represent standard deviation of 4 technical replicates.

FIG. 13 shows changes in gene expression of the wild-type and mutant (including cryptic exon) alleles of CEP290 in cells transfected with Cas9 and pairs of gRNAs shown to have in initial qRT-PCR screening. Total RNA was isolated from modified cells and qRT-PCR with Taqman primer-probe sets was used to quantify expression. Expression is normalized to the Beta-Actin housekeeping gene and each sample is normalized to the GFP control sample (cells transfected with only GFP). Error bars represent standard error of the mean of two to six biological replicates.

FIG. 14 shows deletion rates in cells transfected with indicated gRNA pairs and Cas9 as measured by droplet digital PCR (ddPCR). % deletion was calculated by dividing the number of positive droplets in deletion assay by the number of positive droplets in a control assay. Three biological replicates are shown for two different gRNA pairs.

FIG. 15 shows deletion rates in 293T cells transfected with exemplary AAV expression plasmids. pSS10 encodes EFS-driven saCas9 without gRNA. pSS15 and pSS17 encode EFS-driven saCas9 and one U6-driven gRNA, CEP290-64 and CEP290-323 respectively. pSS11 encodes EFS-driven saCas9 and two U6-driven gRNAs, CEP290-64 and CEP290-323 in the same vector. Deletion PCR were performed with gDNA exacted from 293T cells post transfection. The size of the PCR amplicons indicates the presence or absence of deletion events, and the deletion ratio was calculated.

FIG. 16 shows the composition of structural proteins in AAV2 viral preps expressing Cas9. Reference AAV2 vectors (lanes 1 & 2) were obtained from Vector Core at University of North Carolina, Chapel Hill. AAV2-CMV-GFP (lane 3) and AAV2-CMV-saCas9-minpA (lane4) were packaged and purified with “Triple Transfection Protocol” followed by CsCl ultracentrifugation. Titers were obtained by quantitative PCR with primers annealing to the ITR structures on these vectors. Viral preps were denatured and probed with B1 antibody on Western Blots to demonstrate three structural proteins composing AAV2, VP1, VP2, and VP3 respectively.

FIG. 17 depicts the deletion rates in 293T cells transduced with AAV viral vectors at MOI of 1000 viral genome (vg) per cell and 10,000 vg per cell. AAV2 viral vectors were produced with “Triple Transfection Protocol” using pHelper, pRep2Cap2, pSS8 encoding gRNAs CEP290-64 and CEP290-323, and CMV-driven saCas9. Viral preps were titered with primers annealing to ITRs on pSS8. 6 days post transduction, gDNA were extracted from 293T cells. Deletion PCR was carried out on the CEP290 locus, and deletion rates were calculated based on the predicted amplicons. Western blotting was carried out to show the AAV-mediated saCas9 expression in 293T cells (primary antibody: anti-Flag, M2; loading control: anti-alphaTubulin).

FIG. 18A-18B depicts additional exemplary structures of unimolecular gRNA molecules. FIG. 18A (SEQ ID NO: 45) shows an exemplary structure of a unimolecular gRNA molecule derived in part from S. pyogenes as a duplexed structure. FIG. 18B (SEQ ID NO: 2779) shows an exemplary structure of a unimolecular gRNA molecule derived in part from S. aureus as a duplexed structure.

FIGS. 19A-19G depicts the nucleotide sequence of an exemplary recombinant AAV genome containing a CMV promoter. Various components of the recombinant AAV genome are also indicated. N=A, T, G or C. The number of N residues can vary, e.g., from 16 to 26 nucleotides. Upper stand: 5→3′ (SEQ ID NO: 428); lower stand: 3→5′ SEQ ID NO: 445).

FIGS. 20A-20F depicts the nucleotide sequence of an exemplary recombinant AAV genome containing an EFS promoter. Various components of the recombinant AAV genome are also indicated. N=A, T, G or C. The number of N residues can vary, e.g., from 16 to 26 nucleotides. Upper stand: 5→3′ (SEQ ID NO: 429); lower stand: 3→5′ (SEQ ID NO: 446).

FIGS. 21A-21F depicts the nucleotide sequence of an exemplary recombinant AAV genome containing a CRK1 promoter. Various components of the recombinant AAV genome are also indicated. N=A, T, G or C. The number of N residues can vary, e.g., from 16 to 26 nucleotides. Upper stand: 5→3′ (SEQ ID NO: 430); lower stand: 3→5′ (SEQ ID NO: 447).

FIGS. 22A-22F depicts the nucleotide sequence of an exemplary recombinant AAV genome containing a CRX promoter. Various components of the recombinant AAV genome are also indicated. N=A, T, G or C. The number of N residues can vary, e.g., from 16 to 26 nucleotides. Upper stand: 5→3′ (SEQ ID NO: 431); lower stand: 3→5′ (SEQ ID NO: 448).

FIGS. 23A-23F depicts the nucleotide sequence of an exemplary recombinant AAV genome containing a NRL promoter. Various components of the recombinant AAV genome are also indicated. N=A, T, G or C. The number of N residues can vary, e.g., from 16 to 26 nucleotides. Upper stand: 5→3′ (SEQ ID NO: 432); lower stand: 3→5′ (SEQ ID NO: 449).

FIGS. 24A-24F depicts the nucleotide sequence of an exemplary recombinant AAV genome containing a NRL promoter. Various components of the recombinant AAV genome are also indicated. N=A, T, G or C. The number of N residues can vary, e.g., from 16 to 26 nucleotides. Upper stand: 5→3′ (SEQ ID NO: 433); lower stand: 3→5′ (SEQ ID NO: 450).

FIGS. 25A-D include schematic depictions of exemplary AAV viral genome according to certain embodiments of the disclosure. FIG. 25A shows an AAV genome for use in altering a CEP290 target position which encodes, inter alia, two guide RNAs having specific targeting domains selected from SEQ ID NOs: 389-391, 388, 392, and 394 and an S. aureus Cas9. In certain embodiments, the AAV genome having the configuration illustrated in FIG. 25A may comprise the sequence set forth in SEQ ID NO: 2802. In certain of those embodiments, the genome having the configuration illustrated in FIG. 25A may comprise the sequence set forth in SEQ ID NO: 2803. FIG. 25B shows an AAV genome that may be used for a variety of applications, including without limitation the alteration of the CEP290 target position, encoding two guide RNAs comprising the sequences of SEQ ID NOs: 2785 and 2787 and an S. aureus Cas9. FIG. 25C shows an AAV genome encoding one or two guide RNAs, each driven by a U6 promoter, and an S. aureus Cas9. In the figure, N may be 1 or two. FIG. 25D shows a further annotated version of FIG. 25A, illustrating an AAV genome for use in altering a CEP290 target position which encodes the targeting domains from SEQ ID NOs: 389 and 388 and an S. aureus Cas9. In certain embodiments, the AAV genome having the configuration illustrated in FIG. 25D may comprise the sequence set forth in SEQ ID NO: 2802. In certain of those embodiments, the genome having the configuration illustrated in FIG. 25D may comprise the sequence set forth in SEQ ID NO: 2803.

FIG. 26 illustrates the genome editing strategy implemented in certain embodiments of this disclosure.

FIG. 27A shows a photomicrograph of a mouse retinal explant on a support matrix; retinal tissue is indicated by the arrow. FIG. 27B shows a fluorescence micrograph from a histological section of a mouse retinal explant illustrating AAV transduction of cells in multiple retinal layers with a GFP reporter. FIG. 27C shows a micrograph from a histological section of a primate retinal tissue treated with vehicle. FIG. 27D shows a micrograph from a histological section of a primate retinal tissue treated with AAVS vector encoding S. aureus Cas9 operably linked to the photoreceptor-specific hGRK1 promoter. Dark staining in the outer nuclear layer (ONL) indicates that cells were successfully transduced with AAV and express Cas9.

FIG. 28A and FIG. 28B show expression of Cas9 mRNA and gRNA, respectively, normalized to GAPDH mRNA expression. UT denotes untreated; GRK1-Cas refers to a vector in which Cas9 expression is driven by the photoreceptor-specific hGRK1 promoter; dCMV-Cas and EFS-Cas similarly refer to vectors in which Cas9 expression is driven by the dCMV promoter or the EFS promoter. Conditions in which gRNAs are included in the vector are denoted by the bar captioned “with gRNA.” Light and dark bars depict separate experimental replicates.

FIG. 29 summarizes the edits observed in mouse retinal explants 7 days after transduction with AAVS-mCEPgRNAs-Cas9. Edits were binned into one of three categories: no edit, indel at one of two guide sites, and deletion of sequence between the guide sites. Each bar graph depicts the observed edits as a percentage of sequence reads from individual explants transduced with AAV vectors in which Cas9 was driven by the promoter listed (hGRK1, CMV or EFS).

FIG. 30 summarizes the edits observed in the CEP290 gene in retinal punch samples obtained from cynomolgus monkeys treated with AAV vectors encoding genome editing systems according to the present disclosure.

FIG. 31A depicts a reporter construct that was used to assess the effect of certain editing outcomes, including inversions and deletions, on the IVS26 splicing defect. FIG. 31B depicts the relative levels of GFP reporter expression in WT, IVS26, deletion and inversion conditions, normalized to mCherry expression.

FIG. 32 summarizes the productive CEP290 edits observed in human retinal explants 14 or 28 days after transduction with AAV vectors in which Cas9 was driven by the promoter listed (hGRK1 or CMV).

DETAILED DESCRIPTION Definitions

Unless otherwise specified, each of the following terms has the meaning set forth in this section.

The indefinite articles “a” and “an” denote at least one of the associated noun, and are used interchangeably with the terms “at least one” and “one or more.” For example, the phrase “a module” means at least one module, or one or more modules.

The conjunctions “or” and “and/or” are used interchangeably.

“Domain” as used herein is used to describe segments of a protein or nucleic acid. Unless otherwise indicated, a domain is not required to have any specific functional property.

An “indel” is an insertion and/or deletion in a nucleic acid sequence. An indel may be the product of the repair of a DNA double strand break, such as a double strand break formed by a genome editing system of the present disclosure. An indel is most commonly formed when a break is repaired by an “error prone” repair pathway such as the NHEJ pathway described below. Indels are typically assessed by sequencing (most commonly by “next-gen” or “sequencing-by-synthesis” methods, though Sanger sequencing may still be used) and are quantified by the relative frequency of numerical changes (e.g., ±1, ±2 or more bases) at a site of interest among all sequencing reads. DNA samples for sequencing can be prepared by a variety of methods known in the art, and may involve the amplification of sites of interest by polymerase chain reaction (PCR) or the capture of DNA ends generated by double strand breaks, as in the GUIDEseq process described in Tsai 2016 (incorporated by reference herein). Other sample preparation methods are known in the art. Indels may also be assessed by other methods, including in situ hybridization methods such as the FiberComb™ system commercialized by Genomic Vision (Bagneux, France), and other methods known in the art.

“CEP290 target position” and “CEP290 target site” are used interchangeably herein to refer to a nucleotide or nucleotides in or near the CEP290 gene that are targeted for alteration using the methods described herein. In certain embodiments, a mutation at one or more of these nucleotides is associated with a CEP290 associated disease. The terms “CEP290 target position” and “CEP290 target site” are also used herein to refer to these mutations. For example, the IVS26 mutation is one non-limiting embodiment of a CEP290 target position/target site.

Calculations of homology or sequence identity between two sequences (the terms are used interchangeably herein) are performed as follows. The sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The optimal alignment is determined as the best score using the GAP program in the GCG software package with a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences.

“Governing gRNA molecule” as used herein refers to a gRNA molecule that comprises a targeting domain that is complementary to a target domain on a nucleic acid that comprises a sequence that encodes a component of the CRISPR/Cas system that is introduced into a cell or subject. A governing gRNA does not target an endogenous cell or subject sequence. In an embodiment, a governing gRNA molecule comprises a targeting domain that is complementary with a target sequence on: (a) a nucleic acid that encodes a Cas9 molecule; (b) a nucleic acid that encodes a gRNA which comprises a targeting domain that targets the CEP290 gene (a target gene gRNA); or on more than one nucleic acid that encodes a CRISPR/Cas component, e.g., both (a) and (b). In an embodiment, a nucleic acid molecule that encodes a CRISPR/Cas component, e.g., that encodes a Cas9 molecule or a target gene gRNA, comprises more than one target domain that is complementary with a governing gRNA targeting domain. While not wishing to be bound by theory, it is believed that a governing gRNA molecule complexes with a Cas9 molecule and results in Cas9 mediated inactivation of the targeted nucleic acid, e.g., by cleavage or by binding to the nucleic acid, and results in cessation or reduction of the production of a CRISPR/Cas system component. In an embodiment, the Cas9 molecule forms two complexes: a complex comprising a Cas9 molecule with a target gene gRNA, which complex will alter the CEP290 gene; and a complex comprising a Cas9 molecule with a governing gRNA molecule, which complex will act to prevent further production of a CRISPR/Cas system component, e.g., a Cas9 molecule or a target gene gRNA molecule. In an embodiment, a governing gRNA molecule/Cas9 molecule complex binds to or promotes cleavage of a control region sequence, e.g., a promoter, operably linked to a sequence that encodes a Cas9 molecule, a sequence that encodes a transcribed region, an exon, or an intron, for the Cas9 molecule. In an embodiment, a governing gRNA molecule/Cas9 molecule complex binds to or promotes cleavage of a control region sequence, e.g., a promoter, operably linked to a gRNA molecule, or a sequence that encodes the gRNA molecule. In an embodiment, the governing gRNA, e.g., a Cas9-targeting governing gRNA molecule, or a target gene gRNA-targeting governing gRNA molecule, limits the effect of the Cas9 molecule/target gene gRNA molecule complex-mediated gene targeting. In an embodiment, a governing gRNA places temporal, level of expression, or other limits, on activity of the Cas9 molecule/target gene gRNA molecule complex. In an embodiment, a governing gRNA reduces off-target or other unwanted activity. In an embodiment, a governing gRNA molecule inhibits, e.g., entirely or substantially entirely inhibits, the production of a component of the Cas9 system and thereby limits, or governs, its activity.

“Modulator” as used herein refers to an entity, e.g., a drug that can alter the activity (e.g., enzymatic activity, transcriptional activity, or translational activity), amount, distribution, or structure of a subject molecule or genetic sequence. In an embodiment, modulation comprises cleavage, e.g., breaking of a covalent or non-covalent bond, or the forming of a covalent or non-covalent bond, e.g., the attachment of a moiety, to the subject molecule. In an embodiment, a modulator alters the, three dimensional, secondary, tertiary, or quaternary structure, of a subject molecule. A modulator can increase, decrease, initiate, or eliminate a subject activity.

“Large molecule” as used herein refers to a molecule having a molecular weight of at least 2, 3, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 kD. Large molecules include proteins, polypeptides, nucleic acids, biologics, and carbohydrates.

“Polypeptide” as used herein refers to a polymer of amino acids having less than 100 amino acid residues. In an embodiment, it has less than 50, 20, or 10 amino acid residues.

“Non-homologous end joining” or “NHEJ”, as used herein, refers to ligation mediated repair and/or non-template mediated repair including, e.g., canonical NHEJ (cNHEJ), alternative NHEJ (altNHEJ), microhomology-mediated end joining (MMEJ), single-strand annealing (SSA), and synthesis-dependent microhomology-mediated end joining (SD-MMEJ).

“Reference molecule”, e.g., a reference Cas9 molecule or reference gRNA, as used herein refers to a molecule to which a subject molecule, e.g., a subject Cas9 molecule of subject gRNA molecule, e.g., a modified or candidate Cas9 molecule is compared. For example, a Cas9 molecule can be characterized as having no more than 10% of the nuclease activity of a reference Cas9 molecule. Examples of reference Cas9 molecules include naturally occurring unmodified Cas9 molecules, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S. pyogenes, S. aureus, or S. thermophilus. In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology with the Cas9 molecule to which it is being compared. In an embodiment, the reference Cas9 molecule is a sequence, e.g., a naturally occurring or known sequence, which is the parental form on which a change, e.g., a mutation has been made.

“Replacement”, or “replaced”, as used herein with reference to a modification of a molecule does not require a process limitation but merely indicates that the replacement entity is present.

“Small molecule” as used herein refers to a compound having a molecular weight less than about 2 kD, e.g., less than about 2 kD, less than about 1.5 kD, less than about 1 kD, or less than about 0.75 kD.

“Subject” as used herein means a human, mouse, or non-human primate. A human subject can be any age (e.g., an infant, child, young adult, or adult), and may suffer from a disease, or may be in need of alteration of a gene.

“Treat,” “treating,” and “treatment” as used herein mean the treatment of a disease in a subject (e.g., a human subject), including one or more of inhibiting the disease, i.e., arresting or preventing its development or progression; relieving the disease, i.e., causing regression of the disease state; relieving one or more symptoms of the disease; and curing the disease.

“Prevent,” “preventing,” and “prevention” as used herein means the prevention of a disease in a subject, e.g., in a human, including (a) avoiding or precluding the disease; (b) affecting the predisposition toward the disease; (c) preventing or delaying the onset of at least one symptom of the disease.

The terms “polynucleotide”, “nucleotide sequence”, “nucleic acid”, “nucleic acid molecule”, “nucleic acid sequence”, and “oligonucleotide” as used herein refer to a series of nucleotide bases (also called “nucleotides”) in DNA and RNA, and mean any chain of two or more nucleotides. The polynucleotides can be chimeric mixtures or derivatives or modified versions thereof, single-stranded or double-stranded. The oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone, for example, to improve stability of the molecule, its hybridization parameters, etc. A nucleotide sequence typically carries genetic information, including the information used by cellular machinery to make proteins and enzymes. These terms include double- or single-stranded genomic DNA, RNA, any synthetic and genetically manipulated polynucleotide, and both sense and antisense polynucleotides. This also includes nucleic acids containing modified bases.

“X” as used herein in the context of an amino acid sequence, refers to any amino acid (e.g., any of the twenty natural amino acids) unless otherwise specified.

Conventional IUPAC notation is used in nucleotide sequences presented herein, as shown in Table 1, below (see also Cornish-Bowden 1985, incorporated by reference herein). It should be noted, however, that “T” denotes “Thymine or Uracil” insofar as a given sequence (such as a gRNA sequence) may be encoded by either DNA or RNA.

TABLE 1 IUPAC nucleic acid notation Character Base A Adenine T Thymine G Guanine C Cytosine U Uracil K G or T/U M A or C R A or G Y C or T/U S C or G W A or T/U B C, G, or T/U V A, C, or G H A, C, or T/U D A, G, or T/U N A, C, G, or T/U

The terms “protein,” “peptide” and “polypeptide” are used interchangeably herein to refer to a sequential chain of amino acids linked together via peptide bonds. The terms include individual proteins, groups or complexes of proteins that associate together, as well as fragments, variants, derivatives and analogs of such proteins. Peptide sequences are presented using conventional notation, beginning with the amino or N-terminus on the left, and proceeding to the carboxyl or C-terminus on the right. Standard one-letter or three-letter abbreviations may be used.

Methods of Altering CEP290

CEP290 encodes a centrosomal protein that plays a role in centrosome and cilia development. The CEP290 gene is involved in forming cilia around cells, particularly in the photoreceptors at the back of the retina, which are needed to detect light and color.

Disclosed herein are methods and compositions for altering the LCA10 target position in the CEP290 gene. LCA10 target position can be altered (e.g., corrected) by gene editing, e.g., using CRISPR-Cas9 mediated methods. The alteration (e.g., correction) of the mutant CEP290 gene can be mediated by any mechanism. Exemplary mechanisms that can be associated with the alteration (e.g., correction) of the mutant CEP290 gene include, but are not limited to, non-homologous end joining (e.g., classical or alternative), microhomology-mediated end joining (MMEJ), homology-directed repair (e.g., endogenous donor template mediated), SDSA (synthesis dependent strand annealing), single strand annealing or single strand invasion. Methods described herein introduce one or more breaks near the site of the LCA target position (e.g., c.2991+1655A to G) in at least one allele of the CEP290 gene. In an embodiment, the one or more breaks are repaired by NHEJ. During repair of the one or more breaks, DNA sequences are inserted and/or deleted resulting in the loss or destruction of the cryptic splice site resulting from the mutation at the LCA10 target position (e.g., c.2991+1655A to G). The method can include acquiring knowledge of the mutation carried by the subject, e.g., by sequencing the appropriate portion of the CEP290 gene.

Altering the LCA10 target position refers to (1) break-induced introduction of an indel (also referred to herein as NHEJ-mediated introduction of an indel) in close proximity to or including a LCA10 target position (e.g., c.2991+1655A to G), or (2) break-induced deletion (also referred to herein as NHEJ-mediated deletion) of genomic sequence including the mutation at a LCA10 target position (e.g., c.2991+1655A to G). Both approaches give rise to the loss or destruction of the cryptic splice site.

In an embodiment, the method comprises introducing a break-induced indel in close proximity to or including the LCA10 target position (e.g., c.2991+1655A to G). As described herein, in one embodiment, the method comprises the introduction of a double strand break sufficiently close to (e.g., either 5′ or 3′ to) the LCA10 target position, e.g., c.2991+1655A to G, such that the break-induced indel could be reasonably expected to span the mutation. A single gRNAs, e.g., unimolecular (or chimeric) or modular gRNA molecules, is configured to position a double strand break sufficiently close to the LCA10 target position in the CEP290 gene. In an embodiment, the break is positioned to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat. The double strand break may be positioned within 40 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15, 16, 17, 18, 19, 20, 25, 30, 35 or 40 nucleotides) upstream of the LCA10 target position, or within 40 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15, 16, 17, 18, 19, 20, 25, 30, 35 or 40 nucleotides) downstream of the LCA10 target position (see FIG. 9). While not wishing to be bound by theory, in an embodiment, it is believed that NHEJ-mediated repair of the double strand break allows for the NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position.

In another embodiment, the method comprises the introduction of a pair of single strand breaks sufficiently close to (either 5′ or 3′ to, respectively) the mutation at the LCA10 target position (e.g., c.2991+1655A to G) such that the break-induced indel could be reasonably expected to span the mutation. Two gRNAs, e.g., unimolecular (or chimeric) or modular gRNA molecules, are configured to position the two single strand breaks sufficiently close to the LCA10 target position in the CEP290 gene. In an embodiment, the breaks are positioned to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat. In an embodiment, the pair of single strand breaks is positioned within 40 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15, 16, 17, 18, 19, 20, 25, 30, 35 or 40 nucleotides) upstream of the LCA10 target position, or within 40 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15, 16, 17, 18, 19, 20, 25, 30, 35 or 40 nucleotides) downstream of the LCA10 target position (see FIG. 9). While not wishing to be bound by theory, in an embodiment, it is believed that NHEJ mediated repair of the pair of single strand breaks allows for the NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position. In an embodiment, the pair of single strand breaks may be accompanied by an additional double strand break, positioned by a third gRNA molecule, as is discussed below. In another embodiment, the pair of single strand breaks may be accompanied by two additional single strand breaks positioned by a third gRNA molecule and a fourth gRNA molecule, as is discussed below.

In an embodiment, the method comprises introducing a break-induced deletion of genomic sequence including the mutation at the LCA10 target position (e.g., c.2991+1655A to G). As described herein, in one embodiment, the method comprises the introduction of two double strand breaks—one 5′ and the other 3′ to (i.e., flanking) the LCA10 target position. Two gRNAs, e.g., unimolecular (or chimeric) or modular gRNA molecules, are configured to position the two double strand breaks on opposite sides of the LCA10 target position in the CEP290 gene. In an embodiment, the first double strand break is positioned upstream of the LCA10 target position within intron 26 (e.g., within 1654 nucleotides), and the second double strand break is positioned downstream of the LCA10 target position within intron 26 (e.g., within 4183 nucleotides) (see FIG. 10). In an embodiment, the breaks (i.e., the two double strand breaks) are positioned to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat, or the endogenous CEP290 splice sites.

The first double strand break may be positioned as follows:

-   -   (1) upstream of the 5′ end of the Alu repeat in intron 26,     -   (2) between the 3′ end of the Alu repeat and the LCA10 target         position in intron 26, or     -   (3) within the Alu repeat provided that a sufficient length of         the gRNA fall outside of the repeat so as to avoid binding to         other Alu repeats in the genome,         and the second double strand break to be paired with the first         double strand break may be positioned downstream of the LCA10         target position in intron 26.

For example, the first double strand break may be positioned:

-   -   (1) within 1162 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (2) within 1000 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (3) within 900 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (4) within 800 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (5) within 700 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (6) within 600 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (7) within 500 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (8) within 400 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (9) within 300 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (10) within 200 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (11) within 100 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (12) within 50 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (13) within the Alu repeat provided that a sufficient length of         the gRNA falls outside of the repeat so as to avoid binding to         other Alu repeats in the genome,     -   (14) within 40 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15,         16, 17, 18, 19, 20, 25, 30, 35 or 40 nucleotides) upstream of         the LCA10 target position, or     -   (15) within 17 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15,         16 or 17 nucleotides) upstream of the LCA10 target position,         and the second double strand breaks to be paired with the first         double strand break may be positioned:     -   (1) within 4183 nucleotides downstream of the LCA10 target         position,     -   (2) within 4000 nucleotides downstream of the LCA10 target         position,     -   (3) within 3000 nucleotides downstream of the LCA10 target         position,     -   (4) within 2000 nucleotides downstream of the LCA10 target         position,     -   (5) within 1000 nucleotides downstream of the LCA10 target         position,     -   (6) within 700 nucleotides downstream of the LCA10 target         position,     -   (7) within 500 nucleotides downstream of the LCA10 target         position,     -   (8) within 300 nucleotides downstream of the LCA10 target         position,     -   (9) within 100 nucleotides downstream of the LCA10 target         position,     -   (10) within 60 nucleotides downstream of the LCA10 target         position, or     -   (11) within 40 (e.g., 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or         40 nucleotides) nucleotides downstream of the LCA10 target         position.

While not wishing to be bound by theory, in an embodiment, it is believed that the two double strand breaks allow for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene.

The method also comprises the introduction of two sets of breaks, e.g., one double strand break (either 5′ or 3′ to the mutation at the LCA10 target position, e.g., c.2991+1655A to G) and a pair of single strand breaks (on the other side of the LCA10 target position opposite from the double strand break) such that the two sets of breaks are positioned to flank the LCA10 target position. Three gRNAs, e.g., unimolecular (or chimeric) or modular gRNA molecules, are configured to position the one double strand break and the pair of single strand breaks on opposite sides of the LCA10 target position in the CEP290 gene. In an embodiment, the first set of breaks (either the double strand break or the pair of single strand breaks) is positioned upstream of the LCA10 target position within intron 26 (e.g., within 1654 nucleotides), and the second set of breaks (either the double strand break or the pair of single strand breaks) are positioned downstream of the LCA10 target position within intron 26 (e.g., within 4183 nucleotides) (see FIG. 10). In an embodiment, the two sets of breaks (i.e., the double strand break and the pair of single strand breaks) are positioned to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat, or the endogenous CEP290 splice sites.

The first set of breaks (either the double strand break or the pair of single strand breaks) may be positioned:

-   -   (1) upstream of the 5′ end of the Alu repeat in intron 26,     -   (2) between the 3′ end of the Alu repeat and the LCA10 target         position in intron 26, or     -   (3) within the Alu repeat provided that a sufficient length of         the gRNA falls outside of the repeat so as to avoid binding to         other Alu repeats in the genome,         and the second set of breaks to be paired with the first set of         breaks (either the double strand break or the pair of single         strand breaks) may be positioned downstream of the LCA10 target         position in intron 26.

For example, the first set of breaks (either the double strand break or the pair of single strand breaks) may be positioned:

-   -   (1) within 1162 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (2) within 1000 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (3) within 900 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (4) within 800 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (5) within 700 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (6) within 600 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (7) within 500 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (8) within 400 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (9) within 300 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (10) within 200 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (11) within 100 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (12) within 50 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (13) within the Alu repeat provided that a sufficient length of         the gRNA falls outside of the repeat so as to avoid binding to         other Alu repeats in the genome,     -   (14) within 40 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15,         16, 17, 18, 19, 20, 25, 30, 35 or 40 nucleotides) upstream of         the LCA10 target position, or     -   (15) within 17 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15,         16 or 17 nucleotides) upstream of the LCA10 target position,         and the second set of breaks to be paired with the first set of         breaks (either the double strand break or the pair of single         strand breaks) may be positioned:     -   (1) within 4183 nucleotides downstream of the LCA10 target         position,     -   (2) within 4000 nucleotides downstream of the LCA10 target         position,     -   (3) within 3000 nucleotides downstream of the LCA10 target         position,     -   (4) within 2000 nucleotides downstream of the LCA10 target         position,     -   (5) within 1000 nucleotides downstream of the LCA10 target         position,     -   (6) within 700 nucleotides downstream of the LCA10 target         position,     -   (7) within 500 nucleotides downstream of the LCA10 target         position,     -   (8) within 300 nucleotides downstream of the LCA10 target         position,     -   (9) within 100 nucleotides downstream of the LCA10 target         position,     -   (10) within 60 nucleotides downstream of the LCA10 target         position, or     -   (11) within 40 (e.g., 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or         40 nucleotides) nucleotides downstream of the LCA10 target         position.

While not wishing to be bound by theory, it is believed that the two sets of breaks (either the double strand break or the pair of single strand breaks) allow for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene.

The method also comprises the introduction of two sets of breaks, e.g., two pairs of single strand breaks, wherein the two sets of single-stranded breaks are positioned to flank the LCA10 target position. In an embodiment, the first set of breaks (e.g., the first pair of single strand breaks) is 5′ to the mutation at the LCA10 target position (e.g., c.2991+1655A to G) and the second set of breaks (e.g., the second pair of single strand breaks) is 3′ to the mutation at the LCA10 target position. Four gRNAs, e.g., unimolecular (or chimeric) or modular gRNA molecules, are configured to position the two pairs of single strand breaks on opposite sides of the LCA10 target position in the CEP290 gene. In an embodiment, the first set of breaks (e.g., the first pair of single strand breaks) is positioned upstream of the LCA10 target position within intron 26 (e.g., within 1654 nucleotides), and the second set of breaks (e.g., the second pair of single strand breaks) is positioned downstream of the LCA10 target position within intron 26 (e.g., within 4183 nucleotides) (see FIG. 10). In an embodiment, the two sets of breaks (i.e., the two pairs of single strand breaks) are positioned to avoid unwanted target chromosome elements, such as repeat elements, e.g., an Alu repeat, or the endogenous CEP290 splice sites.

The first set of breaks (e.g., the first pair of single strand breaks) may be positioned:

-   -   (1) upstream of the 5′ end of the Alu repeat in intron 26,     -   (2) between the 3′ end of the Alu repeat and the LCA10 target         position in intron 26, or     -   (3) within the Alu repeat provided that a sufficient length of         the gRNA falls outside of the repeat so as to avoid binding to         other Alu repeats in the genome,         and the second set of breaks to be paired with the first set of         breaks (e.g., the second pair of single strand breaks) may be         positioned downstream of the LCA10 target position in intron 26.

For example, the first set of breaks (e.g., the first pair of single strand breaks) may be positioned:

-   -   (1) within 1162 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (2) within 1000 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (3) within 900 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (4) within 800 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (5) within 700 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (6) within 600 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (7) within 500 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (8) within 400 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (9) within 300 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (10) within 200 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (11) within 100 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (12) within 50 nucleotides upstream of the 5′ end of the Alu         repeat,     -   (13) within the Alu repeat provided that a sufficient length of         the gRNA falls outside of the repeat so as to avoid binding to         other Alu repeats in the genome,     -   (14) within 40 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15,         16, 17, 18, 19, 20, 25, 30, 35 or 40 nucleotides) upstream of         the LCA10 target position, or     -   (15) within 17 nucleotides (e.g., within 1, 2, 3, 4, 5, 10, 15,         16 or 17 nucleotides) upstream of the LCA10 target position,         and the second set of breaks to be paired with the first set of         breaks (e.g., the second pair of single strand breaks) may be         positioned:     -   (1) within 4183 nucleotides downstream of the LCA10 target         position,     -   (2) within 4000 nucleotides downstream of the LCA10 target         position,     -   (3) within 3000 nucleotides downstream of the LCA10 target         position,     -   (4) within 2000 nucleotides downstream of the LCA10 target         position,     -   (5) within 1000 nucleotides downstream of the LCA10 target         position,     -   (6) within 700 nucleotides downstream of the LCA10 target         position,     -   (7) within 500 nucleotides downstream of the LCA10 target         position,     -   (8) within 300 nucleotides downstream of the LCA10 target         position,     -   (9) within 100 nucleotides downstream of the LCA10 target         position,     -   (10) within 60 nucleotides downstream of the LCA10 target         position, or     -   (11) within 40 (e.g., 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or         40 nucleotides) nucleotides downstream of the LCA10 target         position.

While not wishing to be bound by theory, it is believed that the two sets of breaks (e.g., the two pairs of single strand breaks) allow for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene.

Methods of Treating or Preventing LCA10

Described herein are methods for treating or delaying the onset or progression of Leber's Congenital Amaurosis 10 (LCA10) caused by a c.2991+1655 A to G (adenine to guanine) mutation in the CEP290 gene. The disclosed methods for treating or delaying the onset or progression of LCA10 alter the CEP290 gene by genome editing using a gRNA targeting the LCA10 target position and a Cas9 enzyme. Details on gRNAs targeting the LCA10 target position and Cas9 enzymes are provided below.

In an embodiment, treatment is initiated prior to onset of the disease.

In an embodiment, treatment is initiated after onset of the disease.

In an embodiment, treatment is initiated prior to loss of visual acuity and/or sensitivity to glare.

In an embodiment, treatment is initiated at onset of loss of visual acuity.

In an embodiment, treatment is initiated after onset of loss of visual acuity and/or sensitivity to glare.

In an embodiment, treatment is initiated in utero.

In an embodiment, treatment is initiated after birth.

In an embodiment, treatment is initiated prior to the age of 1.

In an embodiment, treatment is initiated prior to the age of 2.

In an embodiment, treatment is initiated prior to the age of 5.

In an embodiment, treatment is initiated prior to the age of 10.

In an embodiment, treatment is initiated prior to the age of 15.

In an embodiment, treatment is initiated prior to the age of 20.

A subject's vision can evaluated, e.g., prior to treatment, or after treatment, e.g., to monitor the progress of the treatment. In an embodiment, the subject's vision is evaluated prior to treatment, e.g., to determine the need for treatment. In an embodiment, the subject's vision is evaluated after treatment has been initiated, e.g., to access the effectiveness of the treatment. Vision can be evaluated by one or more of: evaluating changes in function relative to the contralateral eye, e.g., by utilizing retinal analytical techniques; by evaluating mean, median and distribution of change in best corrected visual acuity (BCVA); evaluation by Optical Coherence Tomography; evaluation of changes in visual field using perimetry; evaluation by full-field electroretinography (ERG); evaluation by slit lamp examination; evaluation of intraocular pressure; evaluation of autofluorescence, evaluation with fundoscopy; evaluation with fundus photography; evaluation with fluorescein angiography (FA); or evaluation of visual field sensitivity (FFST).

In an embodiment, a subject's vision may be assessed by measuring the subject's mobility, e.g., the subject's ability to maneuver in space.

In an embodiment, treatment is initiated in a subject who has tested positive for a mutation in the CEP290 gene, e.g., prior to disease onset or in the earliest stages of disease.

In an embodiment, a subject has a family member that has been diagnosed with LCA10. For example, the subject has a family member that has been diagnosed with LCA10, and the subject demonstrates a symptom or sign of the disease or has been found to have a mutation in the CEP290 gene.

In an embodiment, a cell (e.g., a retinal cell, e.g., a photoreceptor cell) from a subject suffering from or likely to develop LCA10 is treated ex vivo. In an embodiment, the cell is removed from the subject, altered as described herein, and introduced into, e.g., returned to, the subject.

In an embodiment, a cell (e.g., a retinal cell, e.g., a photoreceptor cell) altered to correct a mutation in the LCA10 target position is introduced into the subject.

In an embodiment, the cell is a retinal cell (e.g., retinal pigment epithelium cell), a photoreceptor cell, a horizontal cell, a bipolar cell, an amacrine cell, or a ganglion cell. In an embodiment, it is contemplated herein that a population of cells (e.g., a population of retinal cells, e.g., a population of photoreceptor cells) from a subject may be contacted ex vivo to alter a mutation in CEP290, e.g., a 2991+1655 A to G. In an embodiment, such cells are introduced to the subject's body to prevent or treat LCA10.

In an embodiment, the population of cells are a population of retinal cells (e.g., retinal pigment epithelium cells), photoreceptor cells, horizontal cells, bipolar cells, amacrine cells, ganglion cells, or a combination thereof.

In an embodiment, the method described herein comprises delivery of gRNA or other components described herein, e.g., a Cas9 molecule, by one or more AAV vectors, e.g., one or more AAV vectors described herein.

I. Genome Editing Systems

The term “genome editing system” refers to any system having RNA-guided DNA editing activity. Genome editing systems of the present disclosure include at least two components adapted from naturally occurring CRISPR systems: a gRNA and an RNA-guided nuclease. These two components form a complex that is capable of associating with a specific nucleic acid sequence in a cell and editing the DNA in or around that nucleic acid sequence, for example by making one or more of a single-strand break (an SSB or nick), a double-strand break (a DSB) and/or a base substitution.

Naturally occurring CRISPR systems are organized evolutionarily into two classes and five types (Makarova 2011, incorporated by reference herein), and while genome editing systems of the present disclosure may adapt components of any type or class of naturally occurring CRISPR system, the embodiments presented herein are generally adapted from Class 2, and type II or V CRISPR systems. Class 2 systems, which encompass types II and V, are characterized by relatively large, multidomain RNA-guided nuclease proteins (e.g., Cas9 or Cpf1) that form ribonucleoprotein (RNP) complexes with gRNAs. gRNAs, which are discussed in greater detail below, can include single crRNAs in the case of Cpf1 or duplexed crRNAs and tracrRNAs in the case of Cas9. RNP complexes, in turn, associate with (i.e., target) and cleave specific loci complementary to a targeting (or spacer) sequence of the crRNA. Genome editing systems according to the present disclosure similarly target and edit cellular DNA sequences. but differ significantly from CRISPR systems occurring in nature. For example, the unimolecular gRNAs described herein do not occur in nature, and both gRNAs and RNA-guided nucleases according to this disclosure can incorporate any number of non-naturally occurring modifications.

Genome editing systems can be implemented in a variety of ways, and different implementations may be suitable for any particular application. For example, a genome editing system is implemented, in certain embodiments, as a protein/RNA complex (a ribonucleoprotein, or RNP), which can be included in a pharmaceutical composition that optionally includes a pharmaceutically acceptable carrier and/or an encapsulating agent, such as a lipid or polymer micro- or nano-particle, micelle, liposome, etc. In other embodiments, a genome editing system is implemented as one or more nucleic acids encoding the RNA-guided nuclease and gRNA components described above (optionally with one or more additional components); in still other embodiments, the genome editing system is implemented as one or more vectors comprising such nucleic acids, for example a viral vector such as an AAV; and in still other embodiments, the genome editing system is implemented as a combination of any of the foregoing. Additional or modified implementations that operate according to the principles set forth herein will be apparent to the skilled artisan and are within the scope of this disclosure.

It should be noted that the genome editing systems of the present invention can be targeted to a single specific nucleotide sequence, or can be targeted to—and capable of editing in parallel—two or more specific nucleotide sequences through the use of two or more gRNAs. The use of two or more gRNAs targeted to different sites is referred to as “multiplexing” throughout this disclosure, and can be employed to target multiple, unrelated target sequences of interest, or to form multiple SSBs and/or DSBs within a single target domain and, in some cases, to generate specific edits within such target domain. For example, this disclosure and International Patent Publication No. WO2015/138510 by Maeder et al. (“Maeder”), which is incorporated by reference herein, both describe a genome editing system for correcting a point mutation (C.2991+1655A to G) in the human CEP290 gene that results in the creation of a cryptic splice site, which in turn reduces or eliminates the function of the gene. The genome editing system of Maeder utilizes two gRNAs targeted to sequences on either side of (i.e., flanking) the point mutation, and forms DSBs that flank the mutation. This, in turn, promotes deletion of the intervening sequence, including the mutation, thereby eliminating the cryptic splice site and restoring normal gene function.

As another example, International Patent Publication No. WO2016/073990 by Cotta-Ramusino et al. (“Cotta-Ramusino”), incorporated by reference herein, describes a genome editing system that utilizes two gRNAs in combination with a Cas9 nickase (a Cas9 that makes a single strand nick such as S. pyogenes D10A), an arrangement termed a “dual-nickase system.” The dual-nickase system of Cotta-Ramusino is configured to make two nicks on opposite strands of a sequence of interest that are offset by one or more nucleotides, which nicks combine to create a double strand break having an overhang (5′ in the case of Cotta-Ramusino, though 3′ overhangs are also possible). The overhang, in turn, can facilitate homology directed repair events in some circumstances. As another example, International Patent Publication No. WO2015/070083 by Zhang et al., incorporated by reference herein, describes a gRNA targeted to a nucleotide sequence encoding Cas9 (referred to as a “governing” gRNA), which can be included in a genome editing system comprising one or more additional gRNAs to permit transient expression of a Cas9 that might otherwise be constitutively expressed, for example in some virally transduced cells. These multiplexing applications are intended to be exemplary, rather than limiting, and the skilled artisan will appreciate that other applications of multiplexing are generally compatible with the genome editing systems described here.

Genome editing systems can, in some instances, form double strand breaks that are repaired by cellular DNA double-strand break mechanisms such as non-homologous end joining (NHEJ), or homology directed repair (HDR). These mechanisms are described throughout the literature (see, e.g., Davis 2014 (describing Alt-HDR), Frit 2014 (describing Alt-NHEJ), and lyama 2013 (describing canonical HDR and NHEJ pathways generally), all of which are incorporated by reference herein).

Where genome editing systems operate by forming DSBs, such systems optionally include one or more components that promote or facilitate a particular mode of double-strand break repair or a particular repair outcome. For example, Cotta-Ramusino also describes genome editing systems in which a single stranded oligonucleotide “donor template” is added; the donor template is incorporated into a target region of cellular DNA that is cleaved by the genome editing system, and can result in a change in the target sequence.

In other cases, genome editing systems modify a target sequence, or modify expression of a gene in or near the target sequence, without causing single- or double-strand breaks. For example, a genome editing system can include an RNA-guided nuclease/cytidine deaminase fusion protein, and can operate by generating targeted C-to-A substitutions. Suitable nuclease/deaminase fusions are described in Komor 2016, which is incorporated by reference. Alternatively, a genome editing system can utilize a cleavage-inactivated (i.e., a “dead”) nuclease, such as a dead Cas9, and can operate by forming stable complexes on one or more targeted regions of cellular DNA, thereby interfering with functions involving the targeted region(s) such as mRNA transcription and chromatin remodeling.

II. gRNA Molecules

The terms guide RNA and gRNA refer to any nucleic acid that promotes the specific association (or “targeting”) of an RNA-guided nuclease such as a Cas9 or a Cpf1 to a target sequence such as a genomic or episomal sequence in a cell. gRNAs can be unimolecular (comprising a single RNA molecule, and referred to alternatively as chimeric), or modular (comprising more than one, and typically two, separate RNA molecules, such as a crRNA and a tracrRNA, which are usually associated with one another, for example by duplexing). gRNAs and their component parts are described throughout the literature (see, e.g., Briner 2014, which is incorporated by reference; see also Cotta-Ramusino).

In bacteria and archea, type II CRISPR systems generally comprise an RNA-guided nuclease protein such as Cas9, a CRISPR RNA (crRNA) that includes a 5′ region that is complementary to a foreign sequence, and a trans-activating crRNA (tracrRNA) that includes a 5′ region that is complementary to, and forms a duplex with, a 3′ region of the crRNA. While not intending to be bound by any theory, it is thought that this duplex facilitates the formation of—and is necessary for the activity of—the Cas9/gRNA complex. As type II CRISPR systems were adapted for use in gene editing, it was discovered that the crRNA and tracrRNA could be joined into a single unimolecular or chimeric gRNA, for example by means of a four nucleotide (e.g., GAAA) “tetraloop” or “linker” sequence bridging complementary regions of the crRNA (at its 3′ end) and the tracrRNA (at its 5′ end) (Mali 2013; Jiang 2013; Jinek 2012; all incorporated by reference herein).

gRNAs, whether unimolecular or modular, include a targeting domain that is fully or partially complementary to a target domain within a target sequence, such as a DNA sequence in the genome of a cell where editing is desired. In certain embodiments, this target sequence encompasses or is proximal to a CEP290 target position. Targeting domains are referred to by various names in the literature, including without limitation “guide sequences” (Hsu 2013, incorporated by reference herein), “complementarity regions” (Cotta-Ramusino), “spacers” (Briner 2014), and generically as “crRNAs” (Jiang 2013). Irrespective of the names they are given, targeting domains are typically 10-30 nucleotides in length, preferably 16-24 nucleotides in length (for example, 16, 17, 18, 19, 20, 21, 22, 23 or 24 nucleotides in length), and are at or near the 5′ terminus of in the case of a Cas9 gRNA, and at or near the 3′ terminus in the case of a Cpf1 gRNA.

In addition to the targeting domains, gRNAs typically (but not necessarily, as discussed below) include a plurality of domains that influence the formation or activity of gRNA/Cas9 complexes. For example, as mentioned above, the duplexed structure formed by first and secondary complementarity domains of a gRNA (also referred to as a repeat:anti-repeat duplex) interacts with the recognition (REC) lobe of Cas9 and may mediate the formation of Cas9/gRNA complexes (Nishimasu 2014; Nishimasu 2015; both incorporated by reference herein). It should be noted that the first and/or second complementarity domains can contain one or more poly-A tracts, which can be recognized by RNA polymerases as a termination signal. The sequence of the first and second complementarity domains are, therefore, optionally modified to eliminate these tracts and promote the complete in vitro transcription of gRNAs, for example through the use of A-G swaps as described in Briner 2014, or A-U swaps. These and other similar modifications to the first and second complementarity domains are within the scope of the present disclosure.

Along with the first and second complementarity domains, Cas9 gRNAs typically include two or more additional duplexed regions that are necessary for nuclease activity in vivo but not necessarily in vitro (Nishimasu 2015). A first stem-loop near the 3′ portion of the second complementarity domain is referred to variously as the “proximal domain” (Cotta-Ramusino) “stem loop 1” (Nishimasu 2014; Nishimasu 2015) and the “nexus” (Briner 2014). One or more additional stem loop structures are generally present near the 3′ end of the gRNA, with the number varying by species: S. pyogenes gRNAs typically include two 3′ stem loops (for a total of four stem loop structures including the repeat:anti-repeat duplex), while s. aureus and other species have only one (for a total of three). A description of conserved stem loop structures (and gRNA structures more generally) organized by species is provided in Briner 2014.

Skilled artisans will appreciate that gRNAs can be modified in a number of ways, some of which are described below, and these modifications are within the scope of disclosure. For economy of presentation in this disclosure, gRNAs may be presented by reference solely to their targeting domain sequences.

A gRNA molecule comprises a number of domains. The gRNA molecule domains are described in more detail below.

Several exemplary gRNA structures, with domains indicated thereon, are provided in FIG. 1. While not wishing to be bound by theory, with regard to the three dimensional form, or intra- or inter-strand interactions of an active form of a gRNA, regions of high complementarity are sometimes shown as duplexes in FIG. 1 and other depictions provided herein.

In an embodiment, a unimolecular, or chimeric, gRNA comprises, preferably from 5′ to 3′:

-   -   a targeting domain (which is complementary to a target nucleic         acid in the CEP290 gene, e.g., a targeting domain from any of         Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables         6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B,         or Table 11);     -   a first complementarity domain;     -   a linking domain;     -   a second complementarity domain (which is complementary to the         first complementarity domain);     -   a proximal domain; and     -   optionally, a tail domain.

In an embodiment, a modular gRNA comprises:

-   -   a first strand comprising, preferably from 5′ to 3′;         -   a targeting domain (which is complementary to a target             nucleic acid in the CEP290 gene, e.g., a targeting domain             from Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D,             Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E,             Tables 10A-10B, or Table 11); and         -   a first complementarity domain; and     -   a second strand, comprising, preferably from 5′ to 3′:         -   optionally, a 5′ extension domain;         -   a second complementarity domain;         -   a proximal domain; and         -   optionally, a tail domain.

The domains are discussed briefly below.

Targeting Domain

FIGS. 1A-1G provide examples of the placement of targeting domains.

The targeting domain comprises a nucleotide sequence that is complementary, e.g., at least 80, 85, 90, or 95% complementary, e.g., fully complementary, to the target sequence on the target nucleic acid. The targeting domain is part of an RNA molecule and will therefore comprise the base uracil (U), while any DNA encoding the gRNA molecule will comprise the base thymine (T). While not wishing to be bound by theory, in an embodiment, it is believed that the complementarity of the targeting domain with the target sequence contributes to specificity of the interaction of the gRNA molecule/Cas9 molecule complex with a target nucleic acid. It is understood that in a targeting domain and target sequence pair, the uracil bases in the targeting domain will pair with the adenine bases in the target sequence. In an embodiment, the target domain itself comprises in the 5′ to 3′ direction, an optional secondary domain, and a core domain. In an embodiment, the core domain is fully complementary with the target sequence. In an embodiment, the targeting domain is 5 to 50 nucleotides in length. The strand of the target nucleic acid with which the targeting domain is complementary is referred to herein as the complementary strand. Some or all of the nucleotides of the domain can have a modification, e.g., a modification found in Section VIII herein.

In an embodiment, the targeting domain is 16 nucleotides in length.

In an embodiment, the targeting domain is 17 nucleotides in length.

In an embodiment, the targeting domain is 18 nucleotides in length.

In an embodiment, the targeting domain is 19 nucleotides in length.

In an embodiment, the targeting domain is 20 nucleotides in length.

In an embodiment, the targeting domain is 21 nucleotides in length.

In an embodiment, the targeting domain is 22 nucleotides in length.

In an embodiment, the targeting domain is 23 nucleotides in length.

In an embodiment, the targeting domain is 24 nucleotides in length.

In an embodiment, the targeting domain is 25 nucleotides in length.

In an embodiment, the targeting domain is 26 nucleotides in length.

In an embodiment, the targeting domain comprises 16 nucleotides.

In an embodiment, the targeting domain comprises 17 nucleotides.

In an embodiment, the targeting domain comprises 18 nucleotides.

In an embodiment, the targeting domain comprises 19 nucleotides.

In an embodiment, the targeting domain comprises 20 nucleotides.

In an embodiment, the targeting domain comprises 21 nucleotides.

In an embodiment, the targeting domain comprises 22 nucleotides.

In an embodiment, the targeting domain comprises 23 nucleotides.

In an embodiment, the targeting domain comprises 24 nucleotides.

In an embodiment, the targeting domain comprises 25 nucleotides.

In an embodiment, the targeting domain comprises 26 nucleotides.

Targeting domains are discussed in more detail below.

First Complementarity Domain

FIGS. 1A-1G provide examples of first complementarity domains.

The first complementarity domain is complementary with the second complementarity domain, and in an embodiment, has sufficient complementarity to the second complementarity domain to form a duplexed region under at least some physiological conditions. In an embodiment, the first complementarity domain is 5 to 30 nucleotides in length. In an embodiment, the first complementarity domain is 5 to 25 nucleotides in length. In an embodiment, the first complementary domain is 7 to 25 nucleotides in length. In an embodiment, the first complementary domain is 7 to 22 nucleotides in length. In an embodiment, the first complementary domain is 7 to 18 nucleotides in length. In an embodiment, the first complementary domain is 7 to 15 nucleotides in length. In an embodiment, the first complementary domain is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length.

In an embodiment, the first complementarity domain comprises 3 subdomains, which, in the 5′ to 3′ direction are: a 5′ subdomain, a central subdomain, and a 3′ subdomain. In an embodiment, the 5′ subdomain is 4-9, e.g., 4, 5, 6, 7, 8 or 9 nucleotides in length. In an embodiment, the central subdomain is 1, 2, or 3, e.g., 1, nucleotide in length. In an embodiment, the 3′ subdomain is 3 to 25, e.g., 4-22, 4-18, or 4 to 10, or 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25, nucleotides in length.

The first complementarity domain can share homology with, or be derived from, a naturally occurring first complementarity domain. In an embodiment, it has at least 50% homology with a first complementarity domain disclosed herein, e.g., an S. pyogenes, S. aureus, or S. thermophilus, first complementarity domain.

Some or all of the nucleotides of the domain can have a modification, e.g., a modification found in Section VIII herein.

First complementarity domains are discussed in more detail below.

Linking Domain

FIGS. 1A-1G provide examples of linking domains.

A linking domain serves to link the first complementarity domain with the second complementarity domain of a unimolecular gRNA. The linking domain can link the first and second complementarity domains covalently or non-covalently. In an embodiment, the linkage is covalent. In an embodiment, the linking domain covalently couples the first and second complementarity domains, see, e.g., FIGS. 1B-1E. In an embodiment, the linking domain is, or comprises, a covalent bond interposed between the first complementarity domain and the second complementarity domain. Typically the linking domain comprises one or more, e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides.

In modular gRNA molecules the two molecules are associated by virtue of the hybridization of the complementarity domains see e.g., FIG. 1A.

A wide variety of linking domains are suitable for use in unimolecular gRNA molecules. Linking domains can consist of a covalent bond, or be as short as one or a few nucleotides, e.g., 1, 2, 3, 4, or 5 nucleotides in length. In an embodiment, a linking domain is 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more nucleotides in length. In an embodiment, a linking domain is 2 to 50, 2 to 40, 2 to 30, 2 to 20, 2 to 10, or 2 to 5 nucleotides in length. In an embodiment, a linking domain shares homology with, or is derived from, a naturally occurring sequence, e.g., the sequence of a tracrRNA that is 5′ to the second complementarity domain. In an embodiment, the linking domain has at least 50% homology with a linking domain disclosed herein.

Some or all of the nucleotides of the domain can have a modification, e.g., a modification found in Section VIII herein.

Linking domains are discussed in more detail below.

5′ Extension Domain

In an embodiment, a modular gRNA can comprise additional sequence, 5′ to the second complementarity domain, referred to herein as the 5′ extension domain, see, e.g., FIG. 1A. In an embodiment, the 5′ extension domain is, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, or 2-4 nucleotides in length. In an embodiment, the 5′ extension domain is 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more nucleotides in length.

Second Complementarity Domain

FIGS. 1A-1G provide examples of second complementarity domains.

The second complementarity domain is complementary with the first complementarity domain, and in an embodiment, has sufficient complementarity to the second complementarity domain to form a duplexed region under at least some physiological conditions. In an embodiment, e.g., as shown in FIGS. 1A-1B, the second complementarity domain can include sequence that lacks complementarity with the first complementarity domain, e.g., sequence that loops out from the duplexed region.

In an embodiment, the second complementarity domain is 5 to 27 nucleotides in length. In an embodiment, it is longer than the first complementarity region. In an embodiment the second complementary domain is 7 to 27 nucleotides in length. In an embodiment, the second complementary domain is 7 to 25 nucleotides in length. In an embodiment, the second complementary domain is 7 to 20 nucleotides in length. In an embodiment, the second complementary domain is 7 to 17 nucleotides in length. In an embodiment, the complementary domain is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, the second complementarity domain comprises 3 subdomains, which, in the 5′ to 3′ direction are: a 5′ subdomain, a central subdomain, and a 3′ subdomain. In an embodiment, the 5′ subdomain is 3 to 25, e.g., 4 to 22, 4 to18, or 4 to 10, or 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. In an embodiment, the central subdomain is 1, 2, 3, 4 or 5, e.g., 3, nucleotides in length. In an embodiment, the 3′ subdomain is 4 to 9, e.g., 4, 5, 6, 7, 8 or 9 nucleotides in length.

In an embodiment, the 5′ subdomain and the 3′ subdomain of the first complementarity domain, are respectively, complementary, e.g., fully complementary, with the 3′ subdomain and the 5′ subdomain of the second complementarity domain.

The second complementarity domain can share homology with or be derived from a naturally occurring second complementarity domain. In an embodiment, it has at least 50% homology with a second complementarity domain disclosed herein, e.g., an S. pyogenes, S. aureus, or S. thermophilus, first complementarity domain.

Some or all of the nucleotides of the domain can have a modification, e.g., a modification found in Section VIII herein.

Proximal Domain

FIGS. 1A-1G provide examples of proximal domains.

In an embodiment, the proximal domain is 5 to 20 nucleotides in length. In an embodiment, the proximal domain can share homology with or be derived from a naturally occurring proximal domain. In an embodiment, it has at least 50% homology with a proximal domain disclosed herein, e.g., an S. pyogenes, S. aureus, or S. thermophilus, proximal domain.

Some or all of the nucleotides of the domain can have a modification, e.g., a modification found in Section VIII herein.

Tail Domain

FIGS. 1A-1G provide examples of tail domains.

As can be seen by inspection of the tail domains in FIGS. 1A and 1B-1F, a broad spectrum of tail domains are suitable for use in gRNA molecules. In an embodiment, the tail domain is 0 (absent), 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. In embodiment, the tail domain nucleotides are from or share homology with sequence from the 5′ end of a naturally occurring tail domain, see e.g., FIG. 1D or 1E. In an embodiment, the tail domain includes sequences that are complementary to each other and which, under at least some physiological conditions, form a duplexed region.

In an embodiment, the tail domain is absent or is 1 to 50 nucleotides in length. In an embodiment, the tail domain can share homology with or be derived from a naturally occurring proximal tail domain. In an embodiment, it has at least 50% homology with a tail domain disclosed herein, e.g., an S. pyogenes, S. aureus, or S. thermophilus, tail domain.

In an embodiment, the tail domain includes nucleotides at the 3′ end that are related to the method of in vitro or in vivo transcription. When a T7 promoter is used for in vitro transcription of the gRNA, these nucleotides may be any nucleotides present before the 3′ end of the DNA template. When a U6 promoter is used for in vivo transcription, these nucleotides may be the sequence UUUUUU. When alternate pol-III promoters are used, these nucleotides may be various numbers or uracil bases or may include alternate bases.

The domains of gRNA molecules are described in more detail below.

Targeting Domain

The “targeting domain” of the gRNA is complementary to the “target domain” on the target nucleic acid. The strand of the target nucleic acid comprising the core domain target is referred to herein as the “complementary strand” of the target nucleic acid. Guidance on the selection of targeting domains can be found, e.g., in Fu 2014 and Sternberg 2014.

In an embodiment, the targeting domain is 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length. In the figures and sequence listing provided herein, targeting domains are generally shown with 20 nucleotides. In each of these instances, the targeting domain may actually be shorter or longer as disclosed herein, for example from 16 to 26 nucleotides.

In an embodiment, the targeting domain is 16 nucleotides in length.

In an embodiment, the targeting domain is 17 nucleotides in length.

In an embodiment, the targeting domain is 18 nucleotides in length.

In an embodiment, the targeting domain is 19 nucleotides in length.

In an embodiment, the targeting domain is 20 nucleotides in length.

In an embodiment, the targeting domain is 21 nucleotides in length.

In an embodiment, the targeting domain is 22 nucleotides in length.

In an embodiment, the targeting domain is 23 nucleotides in length.

In an embodiment, the targeting domain is 24 nucleotides in length.

In an embodiment, the targeting domain is 25 nucleotides in length.

In an embodiment, the targeting domain is 26 nucleotides in length.

In an embodiment, the targeting domain comprises 16 nucleotides.

In an embodiment, the targeting domain comprises 17 nucleotides.

In an embodiment, the targeting domain comprises 18 nucleotides.

In an embodiment, the targeting domain comprises 19 nucleotides.

In an embodiment, the targeting domain comprises 20 nucleotides.

In an embodiment, the targeting domain comprises 21 nucleotides.

In an embodiment, the targeting domain comprises 22 nucleotides.

In an embodiment, the targeting domain comprises 23 nucleotides.

In an embodiment, the targeting domain comprises 24 nucleotides.

In an embodiment, the targeting domain comprises 25 nucleotides.

In an embodiment, the targeting domain comprises 26 nucleotides.

In an embodiment, the targeting domain is 10+/−5, 20+/−5, 30+/−5, 40+/−5, 50+/−5, 60+/−5, 70+/−5, 80+/−5, 90+/−5, or 100+/−5 nucleotides, in length.

In an embodiment, the targeting domain is 20+/−5 nucleotides in length.

In an embodiment, the targeting domain is 20+/−10, 30+/−10, 40+/−10, 50+/−10, 60+/−10, 70+/−10, 80+/−10, 90+/−10, or 100+/−10 nucleotides, in length.

In an embodiment, the targeting domain is 30+/−10 nucleotides in length.

In an embodiment, the targeting domain is 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60, 10 to 50, 10 to 40, 10 to 30, 10 to 20 or 10 to 15 nucleotides in length. In other embodiments, the targeting domain is 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 20 to 30, or 20 to 25 nucleotides in length.

Typically the targeting domain has full complementarity with the target sequence. In some embodiments the targeting domain has or includes 1, 2, 3, 4, 5, 6, 7 or 8 nucleotides that are not complementary with the corresponding nucleotide of the targeting domain.

In an embodiment, the target domain includes 1, 2, 3, 4 or 5 nucleotides that are complementary with the corresponding nucleotide of the targeting domain within 5 nucleotides of its 5′ end. In an embodiment, the target domain includes 1, 2, 3, 4 or 5 nucleotides that are complementary with the corresponding nucleotide of the targeting domain within 5 nucleotides of its 3′ end.

In an embodiment, the target domain includes 1, 2, 3, or 4 nucleotides that are not complementary with the corresponding nucleotide of the targeting domain within 5 nucleotides of its 5′ end. In an embodiment, the target domain includes 1, 2, 3, or 4 nucleotides that are not complementary with the corresponding nucleotide of the targeting domain within 5 nucleotides of its 3′ end.

In an embodiment, the degree of complementarity, together with other properties of the gRNA, is sufficient to allow targeting of a Cas9 molecule to the target nucleic acid.

In some embodiments, the targeting domain comprises two consecutive nucleotides that are not complementary to the target domain (“non-complementary nucleotides”), e.g., two consecutive noncomplementary nucleotides that are within 5 nucleotides of the 5′ end of the targeting domain, within 5 nucleotides of the 3′ end of the targeting domain, or more than 5 nucleotides away from one or both ends of the targeting domain.

In an embodiment, no two consecutive nucleotides within 5 nucleotides of the 5′ end of the targeting domain, within 5 nucleotides of the 3′ end of the targeting domain, or within a region that is more than 5 nucleotides away from one or both ends of the targeting domain, are not complementary to the targeting domain.

In an embodiment, there are no noncomplementary nucleotides within 5 nucleotides of the 5′ end of the targeting domain, within 5 nucleotides of the 3′ end of the targeting domain, or within a region that is more than 5 nucleotides away from one or both ends of the targeting domain.

In an embodiment, the targeting domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section VIII. However, in an embodiment, the targeting domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the targeting domain can be modified with a phosphorothioate, or other modification(s) from Section VIII. In an embodiment, a nucleotide of the targeting domain can comprise a 2′ modification, e.g., a 2-acetylation, e.g., a 2′ methylation, or other modification(s) from Section VIII.

In some embodiments, the targeting domain includes 1, 2, 3, 4, 5, 6, 7 or 8 or more modifications. In an embodiment, the targeting domain includes 1, 2, 3, or 4 modifications within 5 nucleotides of its 5′ end. In an embodiment, the targeting domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3′ end.

In some embodiments, the targeting domain comprises modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5′ end of the targeting domain, within 5 nucleotides of the 3′ end of the targeting domain, or more than 5 nucleotides away from one or both ends of the targeting domain.

In an embodiment, no two consecutive nucleotides are modified within 5 nucleotides of the 5′ end of the targeting domain, within 5 nucleotides of the 3′ end of the targeting domain, or within a region that is more than 5 nucleotides away from one or both ends of the targeting domain. In an embodiment, no nucleotide is modified within 5 nucleotides of the 5′ end of the targeting domain, within 5 nucleotides of the 3′ end of the targeting domain, or within a region that is more than 5 nucleotides away from one or both ends of the targeting domain.

Modifications in the targeting domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section V. gRNAs having a candidate targeting domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in a system in Section V. The candidate targeting domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In some embodiments, all of the modified nucleotides are complementary to and capable of hybridizing to corresponding nucleotides present in the target domain. In other embodiments, 1, 2, 3, 4, 5, 6, 7 or 8 or more modified nucleotides are not complementary to or capable of hybridizing to corresponding nucleotides present in the target domain.

In an embodiment, the targeting domain comprises, preferably in the 5′→3′ direction: a secondary domain and a core domain. These domains are discussed in more detail below.

Core Domain and Secondary Domain of the Targeting Domain

The “core domain” of the targeting domain is complementary to the “core domain target” on the target nucleic acid. In an embodiment, the core domain comprises about 8 to about 13 nucleotides from the 3′ end of the targeting domain (e.g., the most 3′ 8 to 13 nucleotides of the targeting domain).

In an embodiment, the secondary domain is absent or optional.

In an embodiment, the core domain and targeting domain, are independently, 6+/−2, 7+/−2, 8+/−2, 9+/−2, 10+/−2, 11+/−2, 12+/−2, 13+/−2, 14+/−2, 15+/−2, 16+−2, 17+/−2, or 18+/−2, nucleotides in length.

In an embodiment, the core domain and targeting domain, are independently, 10+/−2 nucleotides in length.

In an embodiment, the core domain and targeting domain, are independently, 10+/−4 nucleotides in length.

In an embodiment, the core domain and targeting domain, are independently, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18, nucleotides in length.

In an embodiment, the core domain and targeting domain, are independently 3 to 20, 4 to 20, 5 to 20, 6 to 20, 7 to 20, 8 to 20, 9 to 20 10 to 20 or 15 to 20 nucleotides in length.

In an embodiment, the core domain and targeting domain, are independently 3 to 15, e.g., 6 to 15, 7 to 14, 7 to 13, 6 to 12, 7 to 12, 7 to 11, 7 to 10, 8 to 14, 8 to 13, 8 to 12, 8 to 11, 8 to 10 or 8 to 9 nucleotides in length.

The core domain is complementary with the core domain target. Typically the core domain has exact complementarity with the core domain target. In some embodiments, the core domain can have 1, 2, 3, 4 or 5 nucleotides that are not complementary with the corresponding nucleotide of the core domain. In an embodiment, the degree of complementarity, together with other properties of the gRNA, is sufficient to allow targeting of a Cas9 molecule to the target nucleic acid.

The “secondary domain” of the targeting domain of the gRNA is complementary to the “secondary domain target” of the target nucleic acid.

In an embodiment, the secondary domain is positioned 5′ to the core domain.

In an embodiment, the secondary domain is absent or optional.

In an embodiment, if the targeting domain is 26 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 12 to 17 nucleotides in length.

In an embodiment, if the targeting domain is 25 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 12 to 17 nucleotides in length.

In an embodiment, if the targeting domain is 24 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 11 to 16 nucleotides in length.

In an embodiment, if the targeting domain is 23 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 10 to 15 nucleotides in length.

In an embodiment, if the targeting domain is 22 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 9 to 14 nucleotides in length.

In an embodiment, if the targeting domain is 21 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 8 to 13 nucleotides in length.

In an embodiment, if the targeting domain is 20 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 7 to 12 nucleotides in length.

In an embodiment, if the targeting domain is 19 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 6 to 11 nucleotides in length.

In an embodiment, if the targeting domain is 18 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 5 to 10 nucleotides in length.

In an embodiment, if the targeting domain is 17 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 4 to 9 nucleotides in length.

In an embodiment, if the targeting domain is 16 nucleotides in length and the core domain (counted from the 3′ end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 3 to 8 nucleotides in length.

In an embodiment, the secondary domain is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 nucleotides in length.

The secondary domain is complementary with the secondary domain target. Typically the secondary domain has exact complementarity with the secondary domain target. In some embodiments the secondary domain can have 1, 2, 3, 4 or 5 nucleotides that are not complementary with the corresponding nucleotide of the secondary domain. In an embodiment, the degree of complementarity, together with other properties of the gRNA, is sufficient to allow targeting of a Cas9 molecule to the target nucleic acid.

In an embodiment, the core domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section VIII. However, in an embodiment, the core domain comprise one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the core domain can be modified with a phosphorothioate, or other modification(s) from Section VIII. In an embodiment a nucleotide of the core domain can comprise a 2′ modification, e.g., a 2-acetylation, e.g., a 2′ methylation, or other modification(s) from Section VIII. Typically, a core domain will contain no more than 1, 2, or 3 modifications.

Modifications in the core domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section V. gRNA's having a candidate core domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described at Section V. The candidate core domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the secondary domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section VIII. However, in an embodiment, the secondary domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the secondary domain can be modified with a phosphorothioate, or other modification(s) from Section VIII. In an embodiment a nucleotide of the secondary domain can comprise a 2′ modification, e.g., a 2-acetylation, e.g., a 2′ methylation, or other modification(s) from Section VIII. Typically, a secondary domain will contain no more than 1, 2, or 3 modifications.

Modifications in the secondary domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section V. gRNA's having a candidate secondary domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described at Section V. The candidate secondary domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, (1) the degree of complementarity between the core domain and its target, and (2) the degree of complementarity between the secondary domain and its target, may differ. In an embodiment, (1) may be greater (2). In an embodiment, (1) may be less than (2). In an embodiment, (1) and (2) are the same, e.g., each may be completely complementary with its target.

In an embodiment, (1) the number of modification (e.g., modifications from Section VIII) of the nucleotides of the core domain and (2) the number of modification (e.g., modifications from Section VIII) of the nucleotides of the secondary domain, may differ. In an embodiment, (1) may be less than (2). In an embodiment, (1) may be greater than (2). In an embodiment, (1) and (2) may be the same, e.g., each may be free of modifications.

First and Second Complementarity Domains

The first complementarity domain is complementary with the second complementarity domain.

Typically the first domain does not have exact complementarity with the second complementarity domain target. In some embodiments, the first complementarity domain can have 1, 2, 3, 4 or 5 nucleotides that are not complementary with the corresponding nucleotide of the second complementarity domain. In an embodiment, 1, 2, 3, 4, 5 or 6, e.g., 3 nucleotides, will not pair in the duplex, and, e.g., form a non-duplexed or looped-out region. In an embodiment, an unpaired, or loop-out, region, e.g., a loop-out of 3 nucleotides, is present on the second complementarity domain. In an embodiment, the unpaired region begins 1, 2, 3, 4, 5, or 6, e.g., 4, nucleotides from the 5′ end of the second complementarity domain.

In an embodiment, the degree of complementarity, together with other properties of the gRNA, is sufficient to allow targeting of a Cas9 molecule to the target nucleic acid.

In an embodiment, the first and second complementarity domains are:

independently, 6 +/−2, 7+/−2, 8+/−2, 9+/−2, 10+/−2, 11+/−2, 12+/−2, 13+/−2, 14+/−2, 15+/−2, 16+/−2, 17+/−2, 18+/−2, 19+/−2, or 20+/−2, 21+/−2, 22+/−2, 23+/−2, or 24+/−2 nucleotides in length;

independently, 6, 7, 8, 9, 10, 11, 12, 13, 14, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26, nucleotides in length; or

independently, 5 to 24, 5 to 23, 5 to 22, 5 to 21, 5 to 20, 7 to 18, 9 to 16, or 10 to 14 nucleotides in length.

In an embodiment, the second complementarity domain is longer than the first complementarity domain, e.g., 2, 3, 4, 5, or 6, e.g., 6, nucleotides longer.

In an embodiment, the first and second complementary domains, independently, do not comprise modifications, e.g., modifications of the type provided in Section VIII.

In an embodiment, the first and second complementary domains, independently, comprise one or more modifications, e.g., modifications that the render the domain less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the domain can be modified with a phosphorothioate, or other modification(s) from Section VIII. In an embodiment a nucleotide of the domain can comprise a 2′ modification, e.g., a 2-acetylation, e.g., a 2′ methylation, or other modification(s) from Section VIII.

In an embodiment, the first and second complementary domains, independently, include 1, 2, 3, 4, 5, 6, 7 or 8 or more modifications. In an embodiment, the first and second complementary domains, independently, include 1, 2, 3, or 4 modifications within 5 nucleotides of its 5′ end. In an embodiment, the first and second complementary domains, independently, include as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3′ end.

In an embodiment, the first and second complementary domains, independently, include modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5′ end of the domain, within 5 nucleotides of the 3′ end of the domain, or more than 5 nucleotides away from one or both ends of the domain. In an embodiment, the first and second complementary domains, independently, include no two consecutive nucleotides that are modified, within 5 nucleotides of the 5′ end of the domain, within 5 nucleotides of the 3′ end of the domain, or within a region that is more than 5 nucleotides away from one or both ends of the domain. In an embodiment, the first and second complementary domains, independently, include no nucleotide that is modified within 5 nucleotides of the 5′ end of the domain, within 5 nucleotides of the 3′ end of the domain, or within a region that is more than 5 nucleotides away from one or both ends of the domain.

Modifications in a complementarity domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section V. gRNA's having a candidate complementarity domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described in Section V. The candidate complementarity domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the first complementarity domain has at least 60, 70, 80, 85%, 90% or 95% homology with, or differs by no more than 1, 2, 3, 4, 5, or 6 nucleotides from, a reference first complementarity domain, e.g., a naturally occurring, e.g., an S. pyogenes, S. aureus, or S. thermophilus, first complementarity domain, or a first complementarity domain described herein, e.g., from FIGS. 1A-1G.

In an embodiment, the second complementarity domain has at least 60, 70, 80, 85%, 90%, or 95% homology with, or differs by no more than 1, 2, 3, 4, 5, or 6 nucleotides from, a reference second complementarity domain, e.g., a naturally occurring, e.g., an S. pyogenes, S. aureus, or S. thermophilus, second complementarity domain, or a second complementarity domain described herein, e.g., from FIG. 1A-1G.

The duplexed region formed by first and second complementarity domains is typically 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 or 22 base pairs in length (excluding any looped out or unpaired nucleotides).

In some embodiments, the first and second complementarity domains, when duplexed, comprise 11 paired nucleotides, for example, in the gRNA sequence (one paired strand underlined, one bolded):

(SEQ ID NO: 5) NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAA UAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC.

In some embodiments, the first and second complementarity domains, when duplexed, comprise 15 paired nucleotides, for example in the gRNA sequence (one paired strand underlined, one bolded):

(SEQ ID NO: 27) NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGAAAAGCAUAGCA AGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGU CGGUGC.

In some embodiments the first and second complementarity domains, when duplexed, comprise 16 paired nucleotides, for example in the gRNA sequence (one paired strand underlined, one bolded):

(SEQ ID NO: 28) NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGGAAACAGCAUAG CAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGA GUCGGUGC.

In some embodiments the first and second complementarity domains, when duplexed, comprise 21 paired nucleotides, for example in the gRNA sequence (one paired strand underlined, one bolded):

(SEQ ID NO: 29) NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUUUUGGAAACAAA ACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGU GGCACCGAGUCGGUGC.

In some embodiments, nucleotides are exchanged to remove poly-U tracts, for example in the gRNA sequences (exchanged nucleotides underlined):

(SEQ ID NO: 30) NNNNNNNNNNNNNNNNNNNNGUAUUAGAGCUAGAAAUAGCAAGUUAAUAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC; (SEQ ID NO: 31) NNNNNNNNNNNNNNNNNNNNGUUUAAGAGCUAGAAAUAGCAAGUUUAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC; and (SEQ ID NO: 32) NNNNNNNNNNNNNNNNNNNNGUAUUAGAGCUAUGCUGUAUUGGAAACAAU ACAGCAUAGCAAGUUAAUAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGU GGCACCGAGUCGGUGC.

5′ Extension Domain

In an embodiment, a modular gRNA can comprise additional sequence, 5′ to the second complementarity domain. In an embodiment, the 5′ extension domain is 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, or 2 to 4 nucleotides in length. In an embodiment, the 5′ extension domain is 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more nucleotides in length.

In an embodiment, the 5′ extension domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section VIII. However, in an embodiment, the 5′ extension domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the 5′ extension domain can be modified with a phosphorothioate, or other modification(s) from Section VIII. In an embodiment, a nucleotide of the 5′ extension domain can comprise a 2′ modification, e.g., a 2-acetylation, e.g., a 2′ methylation, or other modification(s) from Section VIII.

In some embodiments, the 5′ extension domain can comprise as many as 1, 2, 3, 4, 5, 6, 7 or 8 modifications. In an embodiment, the 5′ extension domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 5′ end, e.g., in a modular gRNA molecule. In an embodiment, the 5′ extension domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3′ end, e.g., in a modular gRNA molecule.

In some embodiments, the 5′ extension domain comprises modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5′ end of the 5′ extension domain, within 5 nucleotides of the 3′ end of the 5′ extension domain, or more than 5 nucleotides away from one or both ends of the 5′ extension domain. In an embodiment, no two consecutive nucleotides are modified within 5 nucleotides of the 5′ end of the 5′ extension domain, within 5 nucleotides of the 3′ end of the 5′ extension domain, or within a region that is more than 5 nucleotides away from one or both ends of the 5′ extension domain. In an embodiment, no nucleotide is modified within 5 nucleotides of the 5′ end of the 5′ extension domain, within 5 nucleotides of the 3′ end of the 5′ extension domain, or within a region that is more than 5 nucleotides away from one or both ends of the 5′ extension domain.

Modifications in the 5′ extension domain can be selected to not interfere with gRNA molecule efficacy, which can be evaluated by testing a candidate modification in the system described in Section V. gRNA's having a candidate 5′ extension domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described at Section V. The candidate 5′ extension domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the 5′ extension domain has at least 60, 70, 80, 85, 90 or 95% homology with, or differs by no more than 1, 2, 3, 4, 5, or 6 nucleotides from, a reference 5′ extension domain, e.g., a naturally occurring, e.g., an S. pyogenes, S. aureus, or S. thermophilus, 5′ extension domain, or a 5′ extension domain described herein, e.g., from FIGS. 1A-1G.

Linking Domain

In a unimolecular gRNA molecule the linking domain is disposed between the first and second complementarity domains. In a modular gRNA molecule, the two molecules are associated with one another by the complementarity domains.

In an embodiment, the linking domain is 10+/−5, 20+/−5, 30+/−5, 40+/−5, 50+/−5, 60+/−5, 70+/−5, 80+/−5, 90+/−5, or 100+/−5 nucleotides, in length.

In an embodiment, the linking domain is 20+/−10, 30+/−10, 40+/−10, 50+/−10, 60+/−10, 70+/−10, 80+/−10, 90+/−10, or 100+/−10 nucleotides, in length.

In an embodiment, the linking domain is 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60, 10 to 50, 10 to 40, 10 to 30, 10 to 20 or 10 to 15 nucleotides in length. In other embodiments, the linking domain is 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 20 to 30, or 20 to 25 nucleotides in length.

In an embodiment, the linking domain is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 17, 18, 19, or 20 nucleotides in length.

In an embodiment, the linking domain is a covalent bond.

In an embodiment, the linking domain comprises a duplexed region, typically adjacent to or within 1, 2, or 3 nucleotides of the 3′ end of the first complementarity domain and/or the 5-end of the second complementarity domain. In an embodiment, the duplexed region can be 20+/−10 base pairs in length. In an embodiment, the duplexed region can be 10+/−5, 15+/−5, 20+/−5, or 30+/−5 base pairs in length. In an embodiment, the duplexed region can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 base pairs in length.

Typically the sequences forming the duplexed region have exact complementarity with one another, though in some embodiments as many as 1, 2, 3, 4, 5, 6, 7 or 8 nucleotides are not complementary with the corresponding nucleotides.

In an embodiment, the linking domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section VIII. However, in an embodiment, the linking domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the linking domain can be modified with a phosphorothioate, or other modification(s) from Section VIII. In an embodiment a nucleotide of the linking domain can comprise a 2′ modification, e.g., a 2-acetylation, e.g., a 2′ methylation, or other modification(s) from Section VIII. In some embodiments, the linking domain can comprise as many as 1, 2, 3, 4, 5, 6, 7 or 8 modifications.

Modifications in a linking domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section V. gRNA's having a candidate linking domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated a system described in Section V. A candidate linking domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the linking domain has at least 60, 70, 80, 85, 90 or 95% homology with, or differs by no more than 1, 2, 3, 4, 5 ,or 6 nucleotides from, a reference linking domain, e.g., a linking domain described herein, e.g., from FIGS. 1A-1G.

Proximal Domain

In an embodiment, the proximal domain is 6 +/−2, 7+/−2, 8+/−2, 9+/−2, 10+/−2, 11+/−2, 12+/−2, 13+/−2, 14+/−2, 14+/−2, 16+/−2, 17+/−2, 18+/−2, 19+/−2, or 20+/−2 nucleotides in length.

In an embodiment, the proximal domain is 6, 7, 8, 9, 10, 11, 12, 13, 14, 14, 16, 17, 18, 19, or 20 nucleotides in length.

In an embodiment, the proximal domain is 5 to 20, 7, to 18, 9 to 16, or 10 to 14 nucleotides in length.

In an embodiment, the proximal domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section VIII. However, in an embodiment, the proximal domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the proximal domain can be modified with a phosphorothioate, or other modification(s) from Section VIII. In an embodiment a nucleotide of the proximal domain can comprise a 2′ modification, e.g., a 2-acetylation, e.g., a 2′ methylation, or other modification(s) from Section VIII.

In some embodiments, the proximal domain can comprise as many as 1, 2, 3, 4, 5, 6, 7 or 8 modifications. In an embodiment, the proximal domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 5′ end, e.g., in a modular gRNA molecule. In an embodiment, the target domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3′ end, e.g., in a modular gRNA molecule.

In some embodiments, the proximal domain comprises modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5′ end of the proximal domain, within 5 nucleotides of the 3′ end of the proximal domain, or more than 5 nucleotides away from one or both ends of the proximal domain. In an embodiment, no two consecutive nucleotides are modified within 5 nucleotides of the 5′ end of the proximal domain, within 5 nucleotides of the 3′ end of the proximal domain, or within a region that is more than 5 nucleotides away from one or both ends of the proximal domain. In an embodiment, no nucleotide is modified within 5 nucleotides of the 5′ end of the proximal domain, within 5 nucleotides of the 3′ end of the proximal domain, or within a region that is more than 5 nucleotides away from one or both ends of the proximal domain.

Modifications in the proximal domain can be selected to not interfere with gRNA molecule efficacy, which can be evaluated by testing a candidate modification in the system described in Section V. gRNA's having a candidate proximal domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described at Section V. The candidate proximal domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the proximal domain has at least 60, 70, 80, 85 90 or 95% homology with, or differs by no more than 1, 2, 3, 4, 5, or 6 nucleotides from, a reference proximal domain, e.g., a naturally occurring, e.g., an S. pyogenes, S. aureus, or S. thermophilus, proximal domain, or a proximal domain described herein, e.g., from FIGS. 1A-1G.

Tail Domain

In an embodiment, the tail domain is 10+/−5, 20+/−5, 30+/−5, 40+/−5, 50+/−5, 60+/−5, 70+/−5, 80+/−5, 90+/−5, or 100+/−5 nucleotides, in length.

In an embodiment, the tail domain is 20+/−5 nucleotides in length.

In an embodiment, the tail domain is 20+/−10, 30+/−10, 40+/−10, 50+/−10, 60+/−10, 70+/−10, 80+/−10, 90+/−10, or 100+/−10 nucleotides, in length.

In an embodiment, the tail domain is 25+/−10 nucleotides in length.

In an embodiment, the tail domain is 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60, 10 to 50, 10 to 40, 10 to 30, 10 to 20 or 10 to 15 nucleotides in length.

In other embodiments, the tail domain is 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 20 to 30, or 20 to 25 nucleotides in length.

In an embodiment, the tail domain is 1 to 20, 1 to 1, 1 to 10, or 1 to 5 nucleotides in length.

In an embodiment, the tail domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section VIII. However, in an embodiment, the tail domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the tail domain can be modified with a phosphorothioate, or other modification(s) from Section VIII. In an embodiment a nucleotide of the tail domain can comprise a 2′ modification, e.g., a 2-acetylation, e.g., a 2′ methylation, or other modification(s) from Section VIII.

In some embodiments, the tail domain can have as many as 1, 2, 3, 4, 5, 6, 7 or 8 modifications. In an embodiment, the target domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 5′ end. In an embodiment, the target domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3′ end.

In an embodiment, the tail domain comprises a tail duplex domain, which can form a tail duplexed region. In an embodiment, the tail duplexed region can be 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 base pairs in length. In an embodiment, a further single stranded domain, exists 3′ to the tail duplexed domain. In an embodiment, this domain is 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. In an embodiment it is 4 to 6 nucleotides in length.

In an embodiment, the tail domain has at least 60, 70, 80, or 90% homology with, or differs by no more than 1, 2, 3, 4, 5 ,or 6 nucleotides from, a reference tail domain, e.g., a naturally occurring, e.g., an S. pyogenes, or S. thermophilus, tail domain, or a tail domain described herein, e.g., from FIGS. 1A-1G.

In an embodiment, the proximal and tail domain, taken together comprise the following sequences:

(SEQ ID NO: 33) AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCU, (SEQ ID NO: 34) AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGGUGC, (SEQ ID NO: 35) AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCGGA UC, (SEQ ID NO: 36) AAGGCUAGUCCGUUAUCAACUUGAAAAAGUG, (SEQ ID NO: 37) AAGGCUAGUCCGUUAUCA, or (SEQ ID NO: 38) AAGGCUAGUCCG.

In an embodiment, the tail domain comprises the 3′ sequence UUUUUU, e.g., if a U6 promoter is used for transcription.

In an embodiment, the tail domain comprises the 3′ sequence UUUU, e.g., if an H1 promoter is used for transcription.

In an embodiment, tail domain comprises variable numbers of 3′ Us depending, e.g., on the termination signal of the pol-III promoter used.

In an embodiment, the tail domain comprises variable 3′ sequence derived from the DNA template if a T7 promoter is used.

In an embodiment, the tail domain comprises variable 3′ sequence derived from the DNA template, e.g., if in vitro transcription is used to generate the RNA molecule.

In an embodiment, the tail domain comprises variable 3′ sequence derived from the DNA template, e., if a pol-II promoter is used to drive transcription.

Modifications in the tail domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section V. gRNAs having a candidate tail domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described in Section V. The candidate tail domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In some embodiments, the tail domain comprises modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5′ end of the tail domain, within 5 nucleotides of the 3′ end of the tail domain, or more than 5 nucleotides away from one or both ends of the tail domain. In an embodiment, no two consecutive nucleotides are modified within 5 nucleotides of the 5′ end of the tail domain, within 5 nucleotides of the 3′ end of the tail domain, or within a region that is more than 5 nucleotides away from one or both ends of the tail domain. In an embodiment, no nucleotide is modified within 5 nucleotides of the 5′ end of the tail domain, within 5 nucleotides of the 3′ end of the tail domain, or within a region that is more than 5 nucleotides away from one or both ends of the tail domain.

In an embodiment a gRNA has the following structure:

5′ [targeting domain]-[first complementarity domain]-[linking domain]-[second complementarity domain]-[proximal domain]-[tail domain]-3′

wherein, the targeting domain comprises a core domain and optionally a secondary domain, and is 10 to 50 nucleotides in length;

the first complementarity domain is 5 to 25 nucleotides in length and, In an embodiment has at least 50, 60, 70, 80, 85, 90 or 95% homology with a reference first complementarity domain disclosed herein;

the linking domain is 1 to 5 nucleotides in length;

the proximal domain is 5 to 20 nucleotides in length and, in an embodiment has at least 50, 60, 70, 80, 85, 90 or 95% homology with a reference proximal domain disclosed herein; and

the tail domain is absent or a nucleotide sequence is 1 to 50 nucleotides in length and, in an embodiment has at least 50, 60, 70, 80, 85, 90 or 95% homology with a reference tail domain disclosed herein.

Exemplary Chimeric gRNAs

In an embodiment, a unimolecular, or chimeric, gRNA comprises, preferably from 5′ to 3′:

a targeting domain, e.g., comprising 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides (which is complementary to a target nucleic acid);

a first complementarity domain;

a linking domain;

a second complementarity domain (which is complementary to the first complementarity domain);

a proximal domain; and

a tail domain,

wherein,

(a) the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides;

(b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain; or

(c) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the sequence from (a), (b), or (c), has at least 60, 75, 80, 85, 90, 95, or 99% homology with the corresponding sequence of a naturally occurring gRNA, or with a gRNA described herein.

In an embodiment, the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides (e.g., 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the unimolecular, or chimeric, gRNA molecule (comprising a targeting domain, a first complementary domain, a linking domain, a second complementary domain, a proximal domain and, optionally, a tail domain) comprises the following sequence in which the targeting domain is depicted as 20 Ns but could be any sequence and range in length from 16 to 26 nucleotides and in which the gRNA sequence is followed by 6 Us, which serve as a termination signal for the U6 promoter, but which could be either absent or fewer in number: NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGG CUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUU (SEQ ID NO: 45). In an embodiment, the unimolecular, or chimeric, gRNA molecule is a S. pyogenes gRNA molecule.

In some embodiments, the unimolecular, or chimeric, gRNA molecule (comprising a targeting domain, a first complementary domain, a linking domain, a second complementary domain, a proximal domain and, optionally, a tail domain) comprises the following sequence in which the targeting domain is depicted as 20 Ns but could be any sequence and range in length from 16 to 26 nucleotides and in which the gRNA sequence is followed by 6 Us, which serve as a termination signal for the U6 promoter, but which could be either absent or fewer in number: NNNNNNNNNNNNNNNNNNNNGUUUUAGUACUCUGGAAACAGAAUCUACUAAAAC AAGGCAAAAUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUUUU (SEQ ID NO: 2779) (corresponding DNA sequence in SEQ ID NO: 2785). In an embodiment, the unimolecular, or chimeric, gRNA molecule is a S. aureus gRNA molecule.

The sequences and structures of exemplary chimeric gRNAs of SEQ ID NOs: 45 and 2779 are shown in FIGS. 18A-18B, respectively.

Exemplary Modular gRNAs

In an embodiment, a modular gRNA comprises:

a first strand comprising, preferably from 5′ to 3′:

a targeting domain, e.g., comprising 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides;

a first complementarity domain; and

a second strand, comprising, preferably from 5′ to 3′:

optionally a 5′ extension domain;

a second complementarity domain;

a proximal domain; and

a tail domain,

wherein:

(a) the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides;

(b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain; or

(c) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the sequence from (a), (b), or (c), has at least 60, 75, 80, 85, 90, 95, or 99% homology with the corresponding sequence of a naturally occurring gRNA, or with a gRNA described herein.

In an embodiment, the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides (e.g., 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

gRNA Modifications

The activity, stability, or other characteristics of gRNAs can be altered through the incorporation of chemical and/or sequential modifications. As one example, transiently expressed or delivered nucleic acids can be prone to degradation by, e.g., cellular nucleases. Accordingly, the gRNAs described herein can contain one or more modified nucleosides or nucleotides which introduce stability toward nucleases. While not wishing to be bound by theory it is also believed that certain modified gRNAs described herein can exhibit a reduced innate immune response when introduced into a population of cells, particularly the cells of the present invention. As noted above, the term “innate immune response” includes a cellular response to exogenous nucleic acids, including single stranded nucleic acids, generally of viral or bacterial origin, which involves the induction of cytokine expression and release, particularly the interferons, and cell death.

One common 3′ end modification is the addition of a poly A tract comprising one or more (and typically 5-200) adenine (A) residues. The poly A tract can be contained in the nucleic acid sequence encoding the gRNA, or can be added to the gRNA during chemical synthesis, or following in vitro transcription using a polyadenosine polymerase (e.g., E. coli Poly(A)Polymerase). In vivo, poly-A tracts can be added to sequences transcribed from DNA vectors through the use of polyadenylation signals. Examples of such signals are provided in Maeder.

III. Methods for Designing gRNAs

Methods for designing gRNAs are described herein, including methods for selecting, designing and validating target domains. Exemplary targeting domains are also provided herein. Targeting Domains discussed herein can be incorporated into the gRNAs described herein.

Methods for selection and validation of target sequences as well as off-target analyses are described, e.g., in Mali 2013; Hsu 2013; Fu 2014; Heigwer 2014; Bae 2014; Xiao 2014.

For example, a software tool can be used to optimize the choice of gRNA within a user's target sequence, e.g., to minimize total off-target activity across the genome. Off target activity may be other than cleavage. For each possible gRNA choice using S. pyogenes Cas9, software tools can identify all potential off-target sequences (preceding either NAG or NGG PAMs) across the genome that contain up to a certain number (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) of mismatched base-pairs. The cleavage efficiency at each off-target sequence can be predicted, e.g., using an experimentally-derived weighting scheme. Each possible gRNA can then ranked according to its total predicted off-target cleavage; the top-ranked gRNAs represent those that are likely to have the greatest on-target and the least off-target cleavage. Other functions, e.g., automated reagent design for gRNA vector construction, primer design for the on-target Surveyor assay, and primer design for high-throughput detection and quantification of off-target cleavage via next-generation sequencing, can also be included in the tool. Candidate gRNA molecules can be evaluated by art-known methods or as described in Section V herein.

Guide RNAs (gRNAs) for use with S. pyogenes, S. aureus and N. meningitidis Cas9s were identified using a DNA sequence searching algorithm. Guide RNA design was carried out using a custom guide RNA design software based on the public tool cas-offinder (Bae 2014). Said custom guide RNA design software scores guides after calculating their genomewide off-target propensity. Typically matches ranging from perfect matches to 7 mismatches are considered for guides ranging in length from 17 to 24. Once the off-target sites are computationally determined, an aggregate score is calculated for each guide and summarized in a tabular output using a web-interface. In addition to identifying potential gRNA sites adjacent to PAM sequences, the software also identifies all PAM adjacent sequences that differ by 1, 2, 3 or more nucleotides from the selected gRNA sites. Genomic DNA sequence for each gene was obtained from the UCSC Genome browser and sequences were screened for repeat elements using the publically available RepeatMasker program. RepeatMasker searches input DNA sequences for repeated elements and regions of low complexity. The output is a detailed annotation of the repeats present in a given query sequence.

Following identification, gRNAs were ranked into tiers based on their distance to the target site, their orthogonality and presence of a 5′ G (based on identification of close matches in the human genome containing a relevant PAM, e.g., in the case of S. pyogenes, a NGG PAM, in the case of S. aureus, NNGRR (e.g., a NNGRRT or NNGRRV) PAM, and in the case of N. meningitides, a NNNNGATT or NNNNGCTT PAM. Orthogonality refers to the number of sequences in the human genome that contain a minimum number of mismatches to the target sequence. A “high level of orthogonality” or “good orthogonality” may, for example, refer to 20-mer gRNAs that have no identical sequences in the human genome besides the intended target, nor any sequences that contain one or two mismatches in the target sequence. Targeting domains with good orthogonality are selected to minimize off-target DNA cleavage.

As an example, for S. pyogenes and N. meningitides targets, 17-mer, or 20-mer gRNAs were designed. As another example, for S. aureus targets, 18-mer, 19-mer, 20-mer, 21-mer, 22-mer, 23-mer and 24-mer gRNAs were designed. Targeting domains, disclosed herein, may comprises the 17-mer described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, e.g., the targeting domains of 18 or more nucleotides may comprise the 17-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. Targeting domains, disclosed herein, may comprises the 18-mer described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, e.g., the targeting domains of 19 or more nucleotides may comprise the 18-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. Targeting domains, disclosed herein, may comprises the 19-mer described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, e.g., the targeting domains of 20 or more nucleotides may comprise the 19-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. Targeting domains, disclosed herein, may comprises the 20-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, e.g., the targeting domains of 21 or more nucleotides may comprise the 20-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. Targeting domains, disclosed herein, may comprises the 21-mer described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, e.g., the targeting domains of 22 or more nucleotides may comprise the 21-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. Targeting domains, disclosed herein, may comprises the 22-mer described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, e.g., the targeting domains of 23 or more nucleotides may comprise the 22-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. Targeting domains, disclosed herein, may comprises the 23-mer described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, e.g., the targeting domains of 24 or more nucleotides may comprise the 23-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11. Targeting domains, disclosed herein, may comprises the 24-mer described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11, e.g., the targeting domains of 25 or more nucleotides may comprise the 24-mer gRNAs described in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11.

gRNAs were identified for both single-gRNA nuclease cleavage and for a dual-gRNA paired “nickase” strategy. Criteria for selecting gRNAs and the determination for which gRNAs can be used for the dual-gRNA paired “nickase” strategy is based on two considerations:

-   -   1. gRNA pairs should be oriented on the DNA such that PAMs are         facing out and cutting with the D10A Cas9 nickase will result in         5′ overhangs.     -   2. An assumption that cleaving with dual nickase pairs will         result in deletion of the entire intervening sequence at a         reasonable frequency. However, cleaving with dual nickase pairs         can also result in indel mutations at the site of only one of         the gRNAs. Candidate pair members can be tested for how         efficiently they remove the entire sequence versus causing indel         mutations at the site of one gRNA.

The Targeting Domains discussed herein can be incorporated into the gRNAs described herein.

Three strategies were utilized to identify gRNAs for use with S. pyogenes, S. aureus and N. meningitidis Cas9 enzymes.

In one strategy, gRNAs were designed for use with S. pyogenes and S. aureus Cas9 enzymes to induce an indel mediated by NHEJ in close proximity to or including the LCA10 target position (e.g., c.2991+1655A to G). The gRNAs were identified and ranked into 4 tiers for S. pyogenes (Tables 2A-2D). The targeting domain for tier 1 gRNA molecules to be used with S. pyogenes Cas9 molecules were selected based on (1) a short distance to the target position, e.g., within 40 bp upstream and 40 bp downstream of the mutation, (2) a high level of orthogonality, and (3) the presence of a 5′ G. For selection of tier 2 gRNAs, a short distance and high orthogonality were required but the presence of a 5′G was not required. Tier 3 uses the same distance restriction and the requirement for a 5′G, but removes the requirement of good orthogonality. Tier 4 uses the same distance restriction but removes the requirement of good orthogonality and the 5′G. The gRNAs were identified and ranked into 4 tiers for S. aureus, when the relevant PAM was NNGRR (Tables 3A-3C). The targeting domain for tier 1 gRNA molecules to be used with S. pyogenes Cas9 molecules were selected based on (1) a short distance to the target position, e.g., within 40 bp upstream and 40 bp downstream of the mutation, (2) a high level of orthogonality, and (3) the presence of a 5′ G. For selection of tier 2 gRNAs, a short distance and high orthogonality were required but the presence of a 5′G was not required. Tier 3 uses the same distance restriction and the requirement for a 5′G, but removes the requirement of good orthogonality. Tier 4 uses the same distance restriction but removes the requirement of good orthogonality and the 5′G. The gRNAs were identified and ranked into 5 tiers for S. aureus when the relevant PAM was NNGRRT or NNGRRV (Tables 7A-7D). The targeting domain for tier 1 gRNA molecules to be used with S. aureus Cas9 molecules were selected based on (1) a short distance to the target position, e.g., within 40 bp upstream and 40 bp downstream of the mutation, (2) a high level of orthogonality, (3) the presence of a 5′ G and (4) PAM was NNGRRT. For selection of tier 2 gRNAs, a short distance and high orthogonality were required but the presence of a 5′G was not required, and PAM was NNGRRT. Tier 3 uses the same distance restriction and the requirement for a 5′G, but removes the requirement of good orthogonality, and PAM was NNGRRT. Tier 4 uses the same distance restriction but removes the requirement of good orthogonality and the 5′G, and PAM was NNGRRT. Tier 5 required a short distance to the target position, e.g., within 40 bp upstream and 40 bp downstream of the mutation and PAM was NNGRRV. Note that tiers are non-inclusive (each gRNA is listed only once for the strategy). In certain instances, no gRNA was identified based on the criteria of the particular tier.

In a second strategy, gRNAs were designed for use with S. pyogenes, S. aureus and N. meningitidis Cas9 molecules to delete a genomic sequence including the mutation at the LCA10 target position (e.g., c.2991+1655A to G), e.g., mediated by NHEJ. The gRNAs were identified and ranked into 4 tiers for S. pyogenes (Tables 4A-4D). The targeting domain to be used with S. pyogenes Cas9 molecules for tier 1 gRNA molecules were selected based on (1) flanking the mutation without targeting unwanted chromosome elements, such as an Alu repeat, e.g., within 400 bp upstream of an Alu repeat or 700 bp downstream of mutation, (2) a high level of orthogonality, and (3) the presence of a 5′ G. For selection of tier 2 gRNAs, a reasonable distance and high orthogonality were required but the presence of a 5′G was not required. Tier 3 uses the same distance restriction and the requirement for a 5′G, but removes the requirement of good orthogonality. Tier 4 uses the same distance restriction but removes the requirement of good orthogonality and the 5′G. The gRNAs were identified and ranked into 4 tiers for S. aureus, when the relevant PAM was NNGRR (Tables 5A-5D). The targeting domain to be used with S. aureus Cas9 molecules for tier 1 gRNA molecules were selected based on (1) flanking the mutation without targeting unwanted chromosome elements, such as an Alu repeat, e.g., within 400 bp upstream of an Alu repeat or 700 bp downstream of mutation, (2) a high level of orthogonality, and (3) the presence of a 5′ G. For selection of tier 2 gRNAs, a reasonable distance and high orthogonality were required but the presence of a 5′G was not required. Tier 3 uses the same distance restriction and the requirement for a 5′G, but removes the requirement of good orthogonality. Tier 4 uses the same distance restriction but removes the requirement of good orthogonality and the 5′G. The gRNAs were identified and ranked into 2 tiers for N. meningitides (Tables 6A-6B). The targeting domain to be used with N. meningitides Cas9 molecules for tier 1 gRNA molecules were selected based on (1) flanking the mutation without targeting unwanted chromosome elements, such as an Alu repeat, e.g., within 400 bp upstream of an Alu repeat or 700 bp downstream of mutation, (2) a high level of orthogonality, and (3) the presence of a 5′ G. For selection of tier 2 gRNAs, a reasonable distance and high orthogonality were required but the presence of a 5′G was not required. Note that tiers are non-inclusive (each gRNA is listed only once for the strategy). In certain instances, no gRNA was identified based on the criteria of the particular tier. In a third strategy, gRNAs were designed for use with S. pyogenes, S. aureus and N. meningitidis Cas9 molecules to delete a genomic sequence including the mutation at the LCA10 target position (e.g., c.2991+1655A to G), e.g., mediated by NHEJ. The gRNAs were identified and ranked into 4 tiers for S. pyogenes (Tables 8A-8D). The targeting domain to be used with S. pyogenes Cas9 enzymes for tier 1 gRNA molecules were selected based on (1) flanking the mutation without targeting unwanted chromosome elements, such as an Alu repeat, e.g., within 1000 bp upstream of an Alu repeat or 1000 bp downstream of mutation, (2) a high level of orthogonality, (3) the presence of a 5′ G and (4) and PAM was NNGRRT. For selection of tier 2 gRNAs, a reasonable distance and high orthogonality were required but the presence of a 5′G was not required, and PAM was NNGRRT. Tier 3 uses the same distance restriction and the requirement for a 5′G, but removes the requirement of good orthogonality, and PAM was NNGRRT. Tier 4 uses the same distance restriction but removes the requirement of good orthogonality and the 5′G, and PAM was NNGRRT. The gRNAs were identified and ranked into 4 tiers for S. aureus, when the relevant PAM was NNGRRT or NNGRRV (Tables 9A-9E). The targeting domain to be used with S. aureus Cas9 enzymes for tier 1 gRNA molecules were selected based on (1) flanking the mutation without targeting unwanted chromosome elements, such as an Alu repeat, e.g., within 1000 bp upstream of an Alu repeat or 1000 bp downstream of mutation, (2) a high level of orthogonality, and (3) the presence of a 5′ G. For selection of tier 2 gRNAs, a reasonable distance and high orthogonality were required but the presence of a 5′G was not required. Tier 3 uses the same distance restriction and the requirement for a 5′G, but removes the requirement of good orthogonality. Tier 4 uses the same distance restriction but removes the requirement of good orthogonality and the 5′G. Tier 5 used the same distance restriction and PAM was NNGRRV. The gRNAs were identified and ranked into 2 tiers for N. meningitides (Tables 10A-10B). The targeting domain to be used with N. meningitides Cas9 molecules for tier 1 gRNA molecules were selected based on (1) flanking the mutation without targeting unwanted chromosome elements, such as an Alu repeat, e.g., within 1000 bp upstream of an Alu repeat or 1000 bp downstream of mutation, (2) a high level of orthogonality, and (3) the presence of a 5′ G. For selection of tier 2 gRNAs, a reasonable distance and high orthogonality were required but the presence of a 5′G was not required. Note that tiers are non-inclusive (each gRNA is listed only once for the strategy). In certain instances, no gRNA was identified based on the criteria of the particular tier.

In an embodiment, when a single gRNA molecule is used to target a Cas9 nickase to create a single strand break to introduce a break-induced indel in close proximity to or including the LCA10 target position, the gRNA is used to target either upstream of (e.g., within 40 bp upstream of the LCA10 target position), or downstream of (e.g., within 40 bp downstream of the LCA10 target position) in the CEP290 gene.

In an embodiment, when a single gRNA molecule is used to target a Cas9 nuclease to create a double strand break to introduce a break-induced indel in close proximity to or including the LCA10 target position, the gRNA is used to target either upstream of (e.g., within 40 bp upstream of the LCA10 target position), or downstream of (e.g., within 40 bp downstream of the LCA10 target position) in the CEP290 gene.

In an embodiment, dual targeting is used to create two double strand breaks to delete a genomic sequence including the mutation at the LCA10 target position, e.g., mediated by NHEJ. In an embodiment, the first and second gRNAs are used target two Cas9 nucleases to flank, e.g., the first of gRNA is used to target upstream of (e.g., within 400 bp upstream of the Alu repeat, or within 40 bp upstream of the LCA10 target position), and the second gRNA is used to target downstream of (e.g., within 700 bp downstream of the LCA10 target position) in the CEP290 gene.

In an embodiment, dual targeting is used to create a double strand break and a pair of single strand breaks to delete a genomic sequence including the mutation at the LCA10 target position, e.g., mediated by NHEJ. In an embodiment, the first, second and third gRNAs are used to target one Cas9 nuclease and two Cas9 nickases to flank, e.g., the first gRNA that will be used with the Cas9 nuclease is used to target upstream of (e.g., within 400 bp upstream of the Alu repeat, or within 40 bp upstream of the LCA10 target position) or downstream of (e.g., within 700 bp downstream) of the LCA10 target position, and the second and third gRNAs that will be used with the Cas9 nickase pair are used to target the opposite side of the LCA10 target position (e.g., within 400 bp upstream of the Alu repeat, within 40 bp upstream of the LCA10 target position, or within 700 bp downstream of the LCA10 target position) in the CEP290 gene.

In an embodiment, when four gRNAs (e.g., two pairs) are used to target four Cas9 nickases to create four single strand breaks to delete genomic sequence including the mutation at the LCA10 target position, e.g., mediated by NHEJ, the first pair and second pair of gRNAs are used to target four Cas9 nickases to flank, e.g., the first pair of gRNAs are used to target upstream of (e.g., within 400 bp upstream of the Alu repeat, or within 40 bp upstream of the LCA10 target position), and the second pair of gRNAs are used to target downstream of (e.g., within 700 bp downstream of the LCA10 target position) in the CEP290 gene.

In an embodiment, dual targeting is utilized to delete genomic sequence including the mutation at the LCA10 target position mediated by NHEJ. It is contemplated herein that in an embodiment any upstream gRNA (e.g., within 400 bp upstream of an Alu repeat, or within 40 bp upstream of the LCA10 target position) in Tables 2A-2C and Tables 4A-4D can be paired with any downstream gRNA (e.g., within 700 downstream of LCA10 target position) in Tables 4A-4D to be used with a S. pyogenes Cas9 molecule to generate dual targeting. Exemplary pairs including selecting a targeting domain that is labeled as upstream from Tables 2A-2C or Tables 4A-4D and a second targeting domain that is labeled as downstream from Tables 4A-4D. In an embodiment, a targeting domain that is labeled as upstream in Tables 2A-2C or Tables 4A-4D can be combined with any of the targeting domains that is labeled as downstream in Tables 4A-4D.

In an embodiment, dual targeting is utilized to delete genomic sequence including the mutation at the LCA10 target position mediated by NHEJ. It is contemplated herein that in an embodiment any upstream gRNA (e.g., within 400 bp upstream of an Alu repeat, or within 40 bp upstream of the LCA10 target position) in Tables 3A-3C and Tables 5A-5D can be paired with any downstream gRNA (e.g., within 700 downstream of LCA10 target position) in Tables 5A-5D to be used with a S. aureus Cas9 molecule to generate dual targeting. Exemplary pairs include selecting a targeting domain that is labeled as upstream from Tables 3A-3C or Tables 5A-5D and a second targeting domain that is labeled as downstream from Tables 5A-5D. In an embodiment, a targeting domain that is labeled as upstream in Tables 3A-3C or Tables 5A-5D can be combined with any of the targeting domains that is labeled as downstream in Tables 5A-5D.

In an embodiment, dual targeting is utilized to delete genomic sequence including the mutation at the LCA10 target position mediated by NHEJ. It is contemplated herein that in an embodiment any upstream gRNA (e.g., within 400 bp upstream of an Alu repeat, or within 40 bp upstream of the LCA10 target position) in Tables 6A-6B can be paired with any downstream gRNA (e.g., within 700 downstream of LCA10 target position) in Tables 6A-6B to be used with a N. meningitidis Cas9 molecule to generate dual targeting. Exemplary pairs include selecting a targeting domain that is labeled as upstream from Tables 6A-6B and a second targeting domain that is labeled as downstream from Tables 6A-6B. In an embodiment, a targeting domain that is labeled as upstream in Tables 6A-6B can be combined with any of the targeting domains that is labeled as downstream in Tables 6A-6B.

In an embodiment, dual targeting (e.g., dual double strand cleavage) is used to create two double strand breaks to delete a genomic sequence including the mutation at the LCA10 target position, e.g., mediated by NHEJ. In an embodiment, the first and second gRNAs are used target two Cas9 nucleases to flank, e.g., the first of gRNA is used to target upstream of (e.g., within 1000 bp upstream of the Alu repeat, or within 40 bp upstream of the LCA10 target position), and the second gRNA is used to target downstream of (e.g., within 1000 bp downstream of the LCA10 target position) in the CEP290 gene.

In an embodiment, dual targeting (e.g., dual double strand cleavage) is used to create a double strand break and a pair of single strand breaks to delete a genomic sequence including the mutation at the LCA10 target position, e.g., mediated by NHEJ. In an embodiment, the first, second and third gRNAs are used to target one Cas9 nuclease and two Cas9 nickases to flank, e.g., the first gRNA that will be used with the Cas9 nuclease is used to target upstream of (e.g., within 1000 bp upstream of the Alu repeat, or within 40 bp upstream of the LCA10 target position) or downstream of (e.g., within 1000 bp downstream) of the LCA10 target position, and the second and third gRNAs that will be used with the Cas9 nickase pair are used to target the opposite side of the LCA10 target position (e.g., within 1000 bp upstream of the Alu repeat, or within 40 bp upstream of the LCA10 target position or within 1000 bp downstream of the LCA10 target position) in the CEP290 gene.

In an embodiment, when four gRNAs (e.g., two pairs) are used to target four Cas9 nickases to create four single strand breaks to delete genomic sequence including the mutation at the LCA10 target position, e.g., mediated by NHEJ, the first pair and second pair of gRNAs are used to target four Cas9 nickases to flank, e.g., the first pair of gRNAs are used to target upstream of (e.g., within 1000 bp upstream of the Alu repeat, or within 40 bp upstream of the LCA10 target position), and the second pair of gRNAs are used to target downstream of (e.g., within 1000 bp downstream of the LCA10 target position) in the CEP290 gene.

In an embodiment, dual targeting is utilized to delete genomic sequence including the mutation at the LCA10 target position, e.g., mediated by NHEJ. It is contemplated herein that in an embodiment any upstream gRNA (e.g., within 1000 bp upstream of an Alu repeat, or within 40 bp upstream of the LCA10 target position) in Tables 2A-2C, Tables 4A-4D, or Tables 8A-8D can be paired with any downstream gRNA (e.g., within 1000 downstream of LCA10 target position) in Tables 2A-2C, Tables 4A-4D, or Tables 8A-8D to be used with a S. pyogenes Cas9 molecule to generate dual targeting. Exemplary pairs including selecting a targeting domain that is labeled as upstream from Tables 2A-2C, Tables 4A-4D, or Tables 8A-8D and a second targeting domain that is labeled as downstream from Tables 2A-2C, Tables 4A-4D, or Tables 8A-8D. In an embodiment, a targeting domain that is labeled as upstream in Tables 2A-2C, Tables 4A-4D, or Tables 8A-8D can be combined with any of the targeting domains that is labeled as downstream in Tables 2A-2C, Tables 4A-4D, or Tables 8A-8D.

In an embodiment, dual targeting is utilized to delete genomic sequence including the mutation at the LCA10 target position mediated by NHEJ. It is contemplated herein that in an embodiment any upstream gRNA (e.g., within 1000 bp upstream of an Alu repeat, or within 40 bp upstream of the LCA10 target position) in Tables 3A-3C, Tables 5A-5D, Tables 7A-7D, or Tables 9A-9E can be paired with any downstream gRNA (e.g., within 1000 downstream of LCA10 target position) in Tables 3A-3C, Tables 5A-5D, Tables 7A-7D, or Tables 9A-9E to be used with a S. aureus Cas9 molecule to generate dual targeting. Exemplary pairs include selecting a targeting domain that is labeled as upstream from Tables 3A-3C, Tables 5A-5D, Tables 7A-7D, or Tables 9A-9E and a second targeting domain that is labeled as downstream from Tables 3A-3C, Tables 5A-5D, Tables 7A-7D, or Tables 9A-9E. In an embodiment, a targeting domain that is labeled as upstream in Tables 3A-3C, Tables 5A-5D, Tables 7A-7D, or Tables 9A-9E can be combined with any of the targeting domains that is labeled as downstream in Tables 3A-3C, Tables 5A-5D, Tables 7A-7D, or Tables 9A-9E.

In an embodiment, dual targeting is utilized to delete genomic sequence including the mutation at the LCA10 target position, e.g., mediated by NHEJ. It is contemplated herein that in an embodiment any upstream gRNA (e.g., within 1000 bp upstream of an Alu repeat, or within 40 bp upstream of the LCA10 target position) in Tables 6A-6B or Tables 10A-10B can be paired with any downstream gRNA (e.g., within 1000 downstream of LCA10 target position) in Tables 6A-6D to be used with a N. meningitidis Cas9 molecule to generate dual targeting. Exemplary pairs include selecting a targeting domain that is labeled as upstream from Tables 6A-6B or Tables 10A-10B and a second targeting domain that is labeled as downstream from Tables 6A-6B or Tables 10A-10B. In an embodiment, a targeting domain that is labeled as upstream in Tables 6A-6B or Tables 10A-10B and can be combined with any of the targeting domains that is labeled as downstream in Tables 6A-6B or Tables 10A-10B.

Any of the targeting domains in the tables described herein can be used with a Cas9 nickase molecule to generate a single strand break.

Any of the targeting domains in the tables described herein can be used with a Cas9 nuclease molecule to generate a double strand break.

In an embodiment, dual targeting (e.g., dual nicking) is used to create two nicks on opposite DNA strands by using S. pyogenes, S. aureus and N. meningitidis Cas9 nickases with two targeting domains that are complementary to opposite DNA strands, e.g., a gRNA comprising any minus strand targeting domain may be paired any gRNA comprising a plus strand targeting domain provided that the two gRNAs are oriented on the DNA such that PAMs face outward and the distance between the 5′ ends of the gRNAs is 0-50 bp. Exemplary nickase pairs including selecting a targeting domain from Group A and a second targeting domain from Group B in Table 2D (for S. pyogenes), or selecting a targeting domain from Group A and a second targeting domain from Group B in Table 7D (for S. aureus). It is contemplated herein that in an embodiment a targeting domain of Group A can be combined with any of the targeting domains of Group B in Table 2D (for S. pyogenes). For example, CEP290-B5 or CEP290-B10 can be combined with CEP290-B1 or CEP290-B6. It is contemplated herein that in an embodiment a targeting domain of Group A can be combined with any of the targeting domains of Group B in Table 7D (for S. aureus). For example, CEP290-12 or CEP290-17 can be combined with CEP290-11 or CEP290-16.

In an embodiment, dual targeting (e.g., dual double strand cleavage) is used to create two double strand breaks by using S. pyogenes, S. aureus and N. meningitidis Cas9 nucleases with two targeting domains. It is contemplated herein that in an embodiment any upstream gRNA of any of Tables 2A-2C, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7C, Tables 8A-8D, Tables 9A-9E, or Tables 10A-10B can be paired with any downstream gRNA of any of Tables 2A-2C, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7C, Tables 8A-8D, Tables 9A-9E, or Tables 10A-10B. Exemplary nucleases pairs are shown in Table 11, e.g., CEP290-323 can be combined with CEP290-11, CEP290-323 can be combined with CEP290-64, CEP290-490 can be combined with CEP290-496, CEP290-490 can be combined with CEP290-502, CEP290-490 can be combined with CEP290-504, CEP290-492 can be combined with CEP290-502, or CEP290-492 can be combined with CEP290-504.

It is contemplated herein that any upstream gRNA described herein may be paired with any downstream gRNA described herein. When an upstream gRNA designed for use with one species of Cas9 is paired with a downstream gRNA designed for use from a different species of Cas9, both Cas9 species are used to generate a single or double-strand break, as desired.

Exemplary Targeting Domains

Table 2A provides targeting domains for NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 40 bases of the LCA10 target position, have good orthogonality, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 2A Target Position DNA Site relative gRNA Name Strand Targeting Domain Length to mutation CEP290-B4 + GAGAUACUCACAAUUACAAC 20 upstream (SEQ ID NO: 395) CEP290-B28 + GAUACUCACAAUUACAACUG 20 upstream (SEQ ID NO: 396)

Table 2B provides targeting domains for NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 40 bases of the LCA10 target position, have good orthogonality, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 2B Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B6 − CUCAUACCUAUCCCUAU 17 downstream (SEQ ID NO: 594) CEP290-B20 + ACACUGCCAAUAGGGAU 17 downstream (SEQ ID NO: 595) CEP290-B10 + CAAUUACAACUGGGGCC 17 upstream (SEQ ID NO: 596) CEP290-B21 + CUAAGACACUGCCAAUA 17 downstream (SEQ ID NO: 597) CEP290-B9 + AUACUCACAAUUACAAC 17 upstream (SEQ ID NO: 598) CEP290-B1 − UAUCUCAUACCUAUCCCUAU 20 downstream (SEQ ID NO: 599) CEP290-B29 + AAGACACUGCCAAUAGGGAU 20 downstream (SEQ ID NO: 600) CEP290-B5 + UCACAAUUACAACUGGGGCC 20 upstream (SEQ ID NO: 601) CEP290-B30 + AGAUACUCACAAUUACAACU 20 upstream (SEQ ID NO: 602)

Table 2C provides targeting domains for NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the fourth tier parameters. The targeting domains are within 40 bases of the LCA10 target position and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 2C Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B22 + ACUAAGACACUGCCAAU (SEQ 17 downstream ID NO: 603) CEP290-B23 + UACUCACAAUUACAACU (SEQ 17 upstream ID NO: 604) CEP290-B24 + ACUCACAAUUACAACUG (SEQ 17 upstream ID NO: 605) CEP290-B25 + ACAACUGGGGCCAGGUG (SEQ 17 upstream ID NO: 606) CEP290-B26 + ACUGGGGCCAGGUGCGG (SEQ 17 upstream ID NO: 607) CEP290-B27 − AUGUGAGCCACCGCACC (SEQ 17 upstream ID NO: 608) CEP290-B31 + AAACUAAGACACUGCCAAUA 20 downstream (SEQ ID NO: 609) CEP290-B32 + AAAACUAAGACACUGCCAAU 20 upstream (SEQ ID NO: 610) CEP290-B33 + AUUACAACUGGGGCCAGGUG 20 upstream (SEQ ID NO: 611) CEP290-B34 + ACAACUGGGGCCAGGUGCGG 20 upstream (SEQ ID NO: 612)

Table 2D provides targeting domains for NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position in the CEP290 gene that can be used for dual targeting. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 (nickase) molecule to generate a single stranded break.

Exemplary nickase pairs including selecting a targeting domain from Group A and a second targeting domain from Group B. It is contemplated herein that a targeting domain of Group A can be combined with any of the targeting domains of Group B. For example, the CEP290-B5 or CEP290-B10 can be combined with CEP290-B1 or CEP290-B6.

TABLE 2D Group A Group B CEP290-B5 CEP290-B1 CEP290-B10 CEP290-B6

Table 3A provides targeting domains for NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 40 bases of the LCA10 target position, have good orthogonality, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 3A Target Position DNA Site relative gRNA Name Strand Targeting Domain Length to mutation CEP290-B1000 + GAGAUACUCACAAUUACAAC 20 upstream (SEQ ID NO: 395) CEP290-B1001 + GAUACUCACAAUUACAA 17 upstream (SEQ ID NO: 397)

Table 3B provides targeting domains for NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 40 bases of the LCA10 target position, have good orthogonality, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 3B Target Position DNA Site relative gRNA Name Strand Targeting Domain Length to mutation CEP290-B1002 + CACUGCCAAUAGGGAUAGGU 20 downstream (SEQ ID NO: 613) CEP290-B1003 + UGCCAAUAGGGAUAGGU (SEQ 17 downstream ID NO: 614) CEP290-B1004 + UGAGAUACUCACAAUUACAA 20 upstream (SEQ ID NO: 615) CEP290-B1005 + AUACUCACAAUUACAAC (SEQ 17 upstream ID NO: 598)

Table 3C provides targeting domains for NHEJ-mediated introduction of an indel in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the fourth tier parameters. The targeting domains are within 40 bases of the LCA10 target position, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 3C Target Position DNA Site relative gRNA Name Strand Targeting Domain Length to mutation CEP290-B1006 − ACCUGGCCCCAGUUGUAAUU 20 upstream (SEQ ID NO: 616) CEP290-B1007 − UGGCCCCAGUUGUAAUU 17 upstream (SEQ ID NO: 617)

Table 4A provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, have good orthogonality, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 4A Target Position DNA Site relative gRNA Name Strand Targeting Domain Length to mutation CEP290-B8 − GCUACCGGUUACCUGAA 17 downstream (SEQ ID NO: 457) CEP290-B217 + GCAGAACUAGUGUAGAC 17 downstream (SEQ ID NO: 458) CEP290-B69 − GUUGAGUAUCUCCUGUU 17 downstream (SEQ ID NO: 459) CEP290-B115 + GAUGCAGAACUAGUGUAGAC 20 downstream (SEQ ID NO: 460) CEP290-B187 + GCUUGAACUCUGUGCCAAAC 20 downstream (SEQ ID NO: 461)

Table 4B provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, have good orthogonality, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 4B Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B269 − AGCUACCGGUUACCUGA 17 downstream (SEQ ID NO: 618) CEP290-B285 + UUUAAGGCGGGGAGUCACAU 20 downstream (SEQ ID NO: 619) CEP290-B3 − AAAGCUACCGGUUACCUGAA 20 downstream (SEQ ID NO: 620) CEP290-B207 − AAAAGCUACCGGUUACCUGA 20 downstream (SEQ ID NO: 621) CEP290-B106 − CUCAUACCUAUCCCUAU (SEQ 17 downstream ID NO: 594) CEP290-B55 + ACACUGCCAAUAGGGAU 17 downstream (SEQ ID NO: 595) CEP290-B138 − UAUCUCAUACCUAUCCCUAU 20 downstream (SEQ ID NO: 599) CEP290-B62 − ACGUGCUCUUUUCUAUAUAU 20 downstream (SEQ ID NO: 622) CEP290-B121 + AUUUGACACCACAUGCACUG 20 downstream (SEQ ID NO: 623) CEP290-B120 − CGUGCUCUUUUCUAUAUAUA 20 downstream (SEQ ID NO: 624) CEP290-B36 − UGGUGUCAAAUAUGGUGCUU 20 downstream (SEQ ID NO: 625) CEP290-B236 + ACUUUUACCCUUCAGGUAAC 20 downstream (SEQ ID NO: 626) CEP290-B70 − AGUGCAUGUGGUGUCAAAUA 20 downstream (SEQ ID NO: 627) CEP290-B177 − UACAUGAGAGUGAUUAGUGG 20 downstream (SEQ ID NO: 628) CEP290-B451 − CGUUGUUCUGAGUAGCUUUC 20 upstream (SEQ ID NO: 629) CEP290-B452 + CCACAAGAUGUCUCUUGCCU 20 upstream (SEQ ID NO: 630) CEP290-B453 − CCUAGGCAAGAGACAUCUUG 20 upstream (SEQ ID NO: 631) CEP290-B454 + UGCCUAGGACUUUCUAAUGC 20 upstream (SEQ ID NO: 632) CEP290-B498 − CGUUGUUCUGAGUAGCUUUC 20 upstream (SEQ ID NO: 629) CEP290-B523 − AUUAGCUCAAAAGCUUUUGC 20 upstream (SEQ ID NO: 633)

Table 4C provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the third tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 4C Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B87 − GCAUGUGGUGUCAAAUA 17 downstream (SEQ ID NO: 479) CEP290-B50 + GAUGACAUGAGGUAAGU 17 downstream (SEQ ID NO: 478) CEP290-B260 + GUCACAUGGGAGUCACA 17 downstream (SEQ ID NO: 500) CEP290-B283 − GAGAGCCACAGUGCAUG 17 downstream (SEQ ID NO: 472) CEP290-B85 − GCUCUUUUCUAUAUAUA 17 downstream (SEQ ID NO: 481) CEP290-B78 + GCUUUUGACAGUUUUUA 17 downstream (SEQ ID NO: 634) CEP290-B292 + GAUAGAGACAGGAAUAA 17 downstream (SEQ ID NO: 476) CEP290-B278 + GGACUUGACUUUUACCCUUC 20 downstream (SEQ ID NO: 485) CEP290-B227 + GGGAGUCACAUGGGAGUCAC 20 downstream (SEQ ID NO: 491) CEP290-B261 − GUGGAGAGCCACAGUGCAUG 20 downstream (SEQ ID NO: 501) CEP290-B182 + GCCUGAACAAGUUUUGAAAC 20 downstream (SEQ ID NO: 480) CEP290-B67 + GGAGUCACAUGGGAGUCACA 20 downstream (SEQ ID NO: 487) CEP290-B216 + GUAAGACUGGAGAUAGAGAC 20 downstream (SEQ ID NO: 497) CEP290-B241 + GCUUUUGACAGUUUUUAAGG 20 downstream (SEQ ID NO: 482) CEP290-B161 + GUUUAGAAUGAUCAUUCUUG 20 downstream (SEQ ID NO: 504) CEP290-B259 + GUAGCUUUUGACAGUUUUUA 20 downstream (SEQ ID NO: 499) CEP290-B79 + GGAGAUAGAGACAGGAAUAA 20 downstream (SEQ ID NO: 635) CEP290-B436 + GUUCUGUCCUCAGUAAA 17 upstream (SEQ ID NO: 503) CEP290-B444 + GGAUAGGACAGAGGACA 17 upstream (SEQ ID NO: 488) CEP290-B445 + GAUGAAAAAUACUCUUU 17 upstream (SEQ ID NO: 477) CEP290-B459 − GAACUCUAUACCUUUUACUG 20 upstream (SEQ ID NO: 466) CEP290-B465 + GUAACAUAAUCACCUCUCUU 20 upstream (SEQ ID NO: 496) CEP290-B473 + GAAAGAUGAAAAAUACUCUU 20 upstream (SEQ ID NO: 462) CEP290-B528 + GUAACAUAAUCACCUCUCUU 20 upstream (SEQ ID NO: 496)

Table 4D provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the fourth tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 4D Target DNA Site gRNA Name Strand Targeting Domain Length CEP290-B233 + AAGGCGGGGAGUCACAU 17 downstream (SEQ ID NO: 636) CEP290-B175 + UAAGGCGGGGAGUCACA 17 downstream (SEQ ID NO: 637) CEP290-B280 + UGAACUCUGUGCCAAAC 17 downstream (SEQ ID NO: 638) CEP290-B92 + CUAAGACACUGCCAAUA 17 downstream (SEQ ID NO: 597) CEP290-B268 + UUUACCCUUCAGGUAAC 17 downstream (SEQ ID NO: 639) CEP290-B154 + UGACACCACAUGCACUG 17 downstream (SEQ ID NO: 640) CEP290-B44 + ACUAAGACACUGCCAAU 17 downstream (SEQ ID NO: 603) CEP290-B231 + UUGCUCUAGAUGACAUG 17 downstream (SEQ ID NO: 641) CEP290-B242 + UGACAGUUUUUAAGGCG 17 downstream (SEQ ID NO: 642) CEP290-B226 − UGUCAAAUAUGGUGCUU 17 downstream (SEQ ID NO: 643) CEP290-B159 + AGUCACAUGGGAGUCAC 17 downstream (SEQ ID NO: 644) CEP290-B222 − AUGAGAGUGAUUAGUGG 17 downstream (SEQ ID NO: 645) CEP290-B274 + UGACAUGAGGUAAGUAG 17 downstream (SEQ ID NO: 646) CEP290-B68 − UACAUGAGAGUGAUUAG 17 downstream (SEQ ID NO: 647) CEP290-B212 + UAAGGAGGAUGUAAGAC 17 downstream (SEQ ID NO: 648) CEP290-B270 + CUUGACUUUUACCCUUC 17 downstream (SEQ ID NO: 649) CEP290-B96 + UCACUGAGCAAAACAAC 17 downstream (SEQ ID NO: 650) CEP290-B104 + AGACUUAUAUUCCAUUA 17 downstream (SEQ ID NO: 651) CEP290-B122 + CAUGGGAGUCACAGGGU 17 downstream (SEQ ID NO: 652) CEP290-B229 + UAGAAUGAUCAUUCUUG 17 downstream (SEQ ID NO: 653) CEP290-B99 + UUGACAGUUUUUAAGGC 17 downstream (SEQ ID NO: 654) CEP290-B7 − AAACUGUCAAAAGCUAC 17 downstream (SEQ ID NO: 655) CEP290-B41 + UCAUUCUUGUGGCAGUA 17 downstream (SEQ ID NO: 2780) CEP290-B37 + AUGACAUGAGGUAAGUA 17 downstream (SEQ ID NO: 656) CEP290-B97 − UGUUUCAAAACUUGUUC 17 downstream (SEQ ID NO: 657) CEP290-B173 − AUAUCUGUCUUCCUUAA 17 downstream (SEQ ID NO: 658) CEP290-B136 + UGAACAAGUUUUGAAAC 17 downstream (SEQ ID NO: 659) CEP290-B71 − UUCUGCAUCUUAUACAU 17 downstream (SEQ ID NO: 660) CEP290-B172 − AUAAGUCUUUUGAUAUA 17 downstream (SEQ ID NO: 661) CEP290-B238 + UUUGACAGUUUUUAAGG 17 downstream (SEQ ID NO: 662) CEP290-B148 − UGCUCUUUUCUAUAUAU 17 downstream (SEQ ID NO: 663) CEP290-B208 + AGACUGGAGAUAGAGAC 17 downstream (SEQ ID NO: 664) CEP290-B53 + CAUAAGAAAGAACACUG 17 downstream (SEQ ID NO: 665) CEP290-B166 + UUCUUGUGGCAGUAAGG 17 downstream (SEQ ID NO: 666) CEP290-B247 − AAGCAUACUUUUUUUAA 17 downstream (SEQ ID NO: 667) CEP290-B245 + CAACUGGAAGAGAGAAA 17 downstream (SEQ ID NO: 668) CEP290-B167 + UAUGCUUAAGAAAAAAA 17 downstream (SEQ ID NO: 669) CEP290-B171 − UUUUAUUAUCUUUAUUG 17 downstream (SEQ ID NO: 670) CEP290-B140 + CUAGAUGACAUGAGGUAAGU 20 downstream (SEQ ID NO: 671) CEP290-B147 + UUUUAAGGCGGGGAGUCACA 20 downstream (SEQ ID NO: 672) CEP290-B253 + AAGACACUGCCAAUAGGGAU 20 downstream (SEQ ID NO: 600) CEP290-B73 − UCCUGUUUCAAAACUUGUUC 20 downstream (SEQ ID NO: 673) CEP290-B206 − UGUGUUGAGUAUCUCCUGUU 20 downstream (SEQ ID NO: 674) CEP290-B57 + CUCUUGCUCUAGAUGACAUG 20 downstream (SEQ ID NO: 675) CEP290-B82 + CAGUAAGGAGGAUGUAAGAC 20 downstream (SEQ ID NO: 676) CEP290-B265 + AGAUGACAUGAGGUAAGUAG 20 downstream (SEQ ID NO: 677) CEP290-B105 + AAUUCACUGAGCAAAACAAC 20 downstream (SEQ ID NO: 678) CEP290-B239 + UCACAUGGGAGUCACAGGGU 20 downstream (SEQ ID NO: 679) CEP290-B180 + UAGAUGACAUGAGGUAAGUA 20 downstream (SEQ ID NO: 680) CEP290-B103 + UUUUGACAGUUUUUAAGGCG 20 downstream (SEQ ID NO: 681) CEP290-B254 − UAAUACAUGAGAGUGAUUAG 20 downstream (SEQ ID NO: 682) CEP290-B134 − UAGUUCUGCAUCUUAUACAU 20 downstream (SEQ ID NO: 683) CEP290-B151 + AAACUAAGACACUGCCAAUA 20 downstream (SEQ ID NO: 609) CEP290-B196 + AAAACUAAGACACUGCCAAU 20 downstream (SEQ ID NO: 610) CEP290-B2 − UAAAAACUGUCAAAAGCUAC 20 downstream (SEQ ID NO: 506) CEP290-B240 + CUUUUGACAGUUUUUAAGGC 20 downstream (SEQ ID NO: 684) CEP290-B116 + AAAAGACUUAUAUUCCAUUA 20 downstream (SEQ ID NO: 685) CEP290-B39 + AUACAUAAGAAAGAACACUG 20 downstream (SEQ ID NO: 686) CEP290-B91 − AAUAUAAGUCUUUUGAUAUA 20 downstream (SEQ ID NO: 687) CEP290-B126 + UGAUCAUUCUUGUGGCAGUA 20 downstream (SEQ ID NO: 688) CEP290-B202 − UACAUAUCUGUCUUCCUUAA 20 downstream (SEQ ID NO: 689) CEP290-B152 − CUUAAGCAUACUUUUUUUAA 20 downstream (SEQ ID NO: 690) CEP290-B77 + AAACAACUGGAAGAGAGAAA 20 downstream (SEQ ID NO: 691) CEP290-B145 + UCAUUCUUGUGGCAGUAAGG 20 downstream (SEQ ID NO: 692) CEP290-B72 + AAGUAUGCUUAAGAAAAAAA 20 downstream (SEQ ID NO: 693) CEP290-B221 − AUUUUUUAUUAUCUUUAUUG 20 downstream (SEQ ID NO: 694) CEP290-B424 + CUAGGACUUUCUAAUGC 17 upstream (SEQ ID NO: 695) CEP290-B425 − AUCUAAGAUCCUUUCAC 17 upstream (SEQ ID NO: 696) CEP290-B426 + UUAUCACCACACUAAAU 17 upstream (SEQ ID NO: 697) CEP290-B427 − AGCUCAAAAGCUUUUGC 17 upstream (SEQ ID NO: 698) CEP290-B428 − UGUUCUGAGUAGCUUUC 17 upstream (SEQ ID NO: 699) CEP290-B429 + ACUUUCUAAUGCUGGAG 17 upstream (SEQ ID NO: 700) CEP290-B430 − CUCUAUACCUUUUACUG 17 upstream (SEQ ID NO: 701) CEP290-B431 + CAAGAUGUCUCUUGCCU 17 upstream (SEQ ID NO: 702) CEP290-B432 − AUUAUGCCUAUUUAGUG 17 upstream (SEQ ID NO: 703) CEP290-B433 + AUGACUCAUAAUUUAGU 17 upstream (SEQ ID NO: 704) CEP290-B434 − UAGAGGCUUAUGGAUUU 17 upstream (SEQ ID NO: 705) CEP290-B435 + UAUUCUACUCCUGUGAA 17 upstream (SEQ ID NO: 706) CEP290-B437 + CUAAUGCUGGAGAGGAU 17 upstream (SEQ ID NO: 707) CEP290-B438 − AGGCAAGAGACAUCUUG 17 upstream (SEQ ID NO: 708) CEP290-B439 + AGCCUCUAUUUCUGAUG 17 upstream (SEQ ID NO: 709) CEP290-B440 − CAGCAUUAGAAAGUCCU 17 upstream (SEQ ID NO: 710) CEP290-B441 − CUGCUUUUGCCAAAGAG 17 upstream (SEQ ID NO: 711) CEP290-B442 + ACAUAAUCACCUCUCUU 17 upstream (SEQ ID NO: 712) CEP290-B443 − UCAGAAAUAGAGGCUUA 17 upstream (SEQ ID NO: 713) CEP290-B446 − UUCCUCAUCAGAAAUAG 17 upstream (SEQ ID NO: 714) CEP290-B447 + ACAGAGGACAUGGAGAA 17 upstream (SEQ ID NO: 715) CEP290-B448 + UGGAGAGGAUAGGACAG 17 upstream (SEQ ID NO: 716) CEP290-B449 + AGGAAGAUGAACAAAUC 17 upstream (SEQ ID NO: 717) CEP290-B450 + AGAUGAAAAAUACUCUU 17 upstream (SEQ ID NO: 718) CEP290-B455 + AGGACUUUCUAAUGCUGGAG 20 upstream (SEQ ID NO: 719) CEP290-B456 − AUUAGCUCAAAAGCUUUUGC 20 upstream (SEQ ID NO: 633) CEP290-B457 − CUCCAGCAUUAGAAAGUCCU 20 upstream (SEQ ID NO: 720) CEP290-B458 + AACAUGACUCAUAAUUUAGU 20 upstream (SEQ ID NO: 721) CEP290-B460 − AUCUUCCUCAUCAGAAAUAG 20 upstream (SEQ ID NO: 722) CEP290-B461 + AUAAGCCUCUAUUUCUGAUG 20 upstream (SEQ ID NO: 723) CEP290-B462 + UCUUAUUCUACUCCUGUGAA 20 upstream (SEQ ID NO: 724) CEP290-B463 − CUGCUGCUUUUGCCAAAGAG 20 upstream (SEQ ID NO: 725) CEP290-B464 + UUUCUAAUGCUGGAGAGGAU 20 upstream (SEQ ID NO: 726) CEP290-B466 + AAAUUAUCACCACACUAAAU 20 upstream (SEQ ID NO: 727) CEP290-B467 + CUUGUUCUGUCCUCAGUAAA 20 upstream (SEQ ID NO: 728) CEP290-B468 − AAAAUUAUGCCUAUUUAGUG 20 upstream (SEQ ID NO: 729) CEP290-B469 − UCAUCAGAAAUAGAGGCUUA 20 upstream (SEQ ID NO: 730) CEP290-B470 − AAAUAGAGGCUUAUGGAUUU 20 upstream (SEQ ID NO: 731) CEP290-B471 + UGCUGGAGAGGAUAGGACAG 20 upstream (SEQ ID NO: 732) CEP290-B472 + AUGAGGAAGAUGAACAAAUC 20 upstream (SEQ ID NO: 733) CEP290-B474 − CUUAUCUAAGAUCCUUUCAC 20 upstream (SEQ ID NO: 734) CEP290-B475 + AGAGGAUAGGACAGAGGACA 20 upstream (SEQ ID NO: 735) CEP290-B476 + AGGACAGAGGACAUGGAGAA 20 upstream (SEQ ID NO: 736) CEP290-B477 + AAAGAUGAAAAAUACUCUUU 20 upstream (SEQ ID NO: 737) CEP290-B495 − AGCUCAAAAGCUUUUGC 17 upstream (SEQ ID NO: 698) CEP290-B529 − UGUUCUGAGUAGCUUUC 17 upstream (SEQ ID NO: 699) CEP290-B513 + AUGACUCAUAAUUUAGU 17 upstream (SEQ ID NO: 704) CEP290-B490 + UAUUCUACUCCUGUGAA 17 upstream (SEQ ID NO: 706) CEP290-B485 − CUGCUUUUGCCAAAGAG 17 upstream (SEQ ID NO: 711) CEP290-B492 + ACAUAAUCACCUCUCUU 17 upstream (SEQ ID NO: 712) CEP290-B506 + AACAUGACUCAUAAUUUAGU 20 upstream (SEQ ID NO: 721) CEP290-B500 + UCUUAUUCUACUCCUGUGAA 20 upstream (SEQ ID NO: 724) CEP290-B521 − CUGCUGCUUUUGCCAAAGAG 20 upstream (SEQ ID NO: 725)

Table 5A provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, have good orthogonality, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 5A Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B1008 + GAAUCCUGAAAGCUACU 17 upstream (SEQ ID NO: 510)

Table 5B provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, have good orthogonality, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 5B Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B1009 − CCUACUUACCUCAUGUCAUC 20 downstream (SEQ ID NO: 747) CEP290-B1010 + CUAUGAGCCAGCAAAAGCUU 20 upstream (SEQ ID NO: 748) CEP290-B1011 − ACGUUGUUCUGAGUAGCUUU 20 upstream (SEQ ID NO: 749) CEP290-B1012 − CAUAGAGACACAUUCAGUAA 20 upstream (SEQ ID NO: 750) CEP290-B1013 − ACUUACCUCAUGUCAUC 17 downstream (SEQ ID NO: 751) CEP290-B1014 + UGAGCCAGCAAAAGCUU 17 upstream (SEQ ID NO: 752) CEP290-B1015 − UUGUUCUGAGUAGCUUU 17 upstream (SEQ ID NO: 753) CEP290-B1016 − AGAGACACAUUCAGUAA 17 upstream (SEQ ID NO: 754) CEP290-B1017 + UUUAAGGCGGGGAGUCACAU 20 downstream (SEQ ID NO: 619) CEP290-B1018 − CAAAAGCUACCGGUUACCUG 20 downstream (SEQ ID NO: 755) CEP290-B1019 + UUUUAAGGCGGGGAGUCACA 20 downstream (SEQ ID NO: 672) CEP290-B1020 − UGUCAAAAGCUACCGGUUAC 20 downstream (SEQ ID NO: 757) CEP290-B1021 + AAGGCGGGGAGUCACAU 17 downstream (SEQ ID NO: 636) CEP290-B1022 − AAGCUACCGGUUACCUG 17 downstream (SEQ ID NO: 758) CEP290-B1023 + UAAGGCGGGGAGUCACA 17 downstream (SEQ ID NO: 637) CEP290-B1024 − CAAAAGCUACCGGUUAC 17 downstream (SEQ ID NO: 759) CEP290-B1025 + UAGGAAUCCUGAAAGCUACU 20 upstream (SEQ ID NO: 760) CEP290-B1026 + CAGAACAACGUUUUCAUUUA 20 upstream (SEQ ID NO: 761) CEP290-B1027 − CAAAAGCUUUUGCUGGCUCA 20 upstream (SEQ ID NO: 762) CEP290-B1028 + AGCAAAAGCUUUUGAGCUAA 20 upstream (SEQ ID NO: 763) CEP290-B1029 + AUCUUAUUCUACUCCUGUGA 20 upstream (SEQ ID NO: 764) CEP290-B1030 + AACAACGUUUUCAUUUA 17 upstream (SEQ ID NO: 765) CEP290-B1031 − AAGCUUUUGCUGGCUCA 17 upstream (SEQ ID NO: 766) CEP290-B1032 + AAAAGCUUUUGAGCUAA 17 upstream (SEQ ID NO: 767) CEP290-B1033 + UUAUUCUACUCCUGUGA 17 upstream (SEQ ID NO: 768)

Table 5C provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the third tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 5C Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B1034 + GAAACAGGAAUAGAAAUUCA 20 downstream (SEQ ID NO: 769) CEP290-B1035 + GAAAGAUGAAAAAUACUCUU 20 upstream (SEQ ID NO: 462) CEP290-B1036 − GAAAUAGAGGCUUAUGGAUU 20 upstream (SEQ ID NO: 547) CEP290-B1037 − GAAUAUAAGUCUUUUGAUAU 20 downstream (SEQ ID NO: 770) CEP290-B1038 + GAGAAAUGGUUCCCUAUAUA 20 downstream (SEQ ID NO: 771) CEP290-B1039 + GAGAGGAUAGGACAGAGGAC 20 upstream (SEQ ID NO: 772) CEP290-B1040 + GAUGAGGAAGAUGAACAAAU 20 upstream (SEQ ID NO: 773) CEP290-B1041 + GAUGCAGAACUAGUGUAGAC 20 downstream (SEQ ID NO: 460) CEP290-B1042 − GAUUUGUUCAUCUUCCUCAU 20 upstream (SEQ ID NO: 774) CEP290-B1043 + GCAGUAAGGAGGAUGUAAGA 20 downstream (SEQ ID NO: 775) CEP290-B1044 + GCCUGAACAAGUUUUGAAAC 20 downstream (SEQ ID NO: 480) CEP290-B1045 + GCUUGAACUCUGUGCCAAAC 20 downstream (SEQ ID NO: 461) CEP290-B1046 − GCUUUCUGCUGCUUUUGCCA 20 upstream (SEQ ID NO: 776) CEP290-B1047 − GCUUUCUGCUGCUUUUGCCA 20 upstream (SEQ ID NO: 776) CEP290-B1048 + GCUUUUGACAGUUUUUAAGG 20 downstream (SEQ ID NO: 482) CEP290-B1049 + GGAAAGAUGAAAAAUACUCU 20 upstream (SEQ ID NO: 778) CEP290-B1050 + GGAGGAUGUAAGACUGGAGA 20 downstream (SEQ ID NO: 779) CEP290-B1051 + GGGGAGUCACAUGGGAGUCA 20 downstream (SEQ ID NO: 573) CEP290-B1052 − GGUGAUUAUGUUACUUUUUA 20 upstream (SEQ ID NO: 780) CEP290-B1053 − GGUGAUUAUGUUACUUUUUA 20 upstream (SEQ ID NO: 780) CEP290-B1054 + GUAAGACUGGAGAUAGAGAC 20 downstream (SEQ ID NO: 497) CEP290-B1055 + GUCACAUGGGAGUCACAGGG 20 downstream (SEQ ID NO: 586) CEP290-B1056 − GUGGUGUCAAAUAUGGUGCU 20 downstream (SEQ ID NO: 782) CEP290-B1057 + GAAAAAAAAGGUAAUGC 17 downstream (SEQ ID NO: 783) CEP290-B1058 + GAAAAGAGCACGUACAA 17 downstream (SEQ ID NO: 784 CEP290-B1059 + GAAUCCUGAAAGCUACU 17 upstream (SEQ ID NO: 510) CEP290-B1060 − GAAUGAUCAUUCUAAAC 17 downstream (SEQ ID NO: 785) CEP290-B1061 + GACAGAGGACAUGGAGA 17 upstream (SEQ ID NO: 786) CEP290-B1062 + GACUUUCUAAUGCUGGA 17 upstream (SEQ ID NO: 787) CEP290-B1063 − GAGAGUGAUUAGUGGUG 17 downstream (SEQ ID NO: 788) CEP290-B1064 + GAGCAAAACAACUGGAA 17 downstream (SEQ ID NO: 789) CEP290-B1065 + GAGGAAGAUGAACAAAU 17 upstream (SEQ ID NO: 790) CEP290-B1066 + GAGUCACAUGGGAGUCA 17 downstream (SEQ ID NO: 791) CEP290-B1067 + GAUCUUAUUCUACUCCU 17 upstream (SEQ ID NO: 792) CEP290-B1068 + GAUCUUAUUCUACUCCU 17 upstream (SEQ ID NO: 792) CEP290-B1069 + GAUGAAAAAUACUCUUU 17 upstream (SEQ ID NO: 477) CEP290-B1070 + GAUGACAUGAGGUAAGU 17 downstream (SEQ ID NO: 478) CEP290-B1071 − GAUUAUGUUACUUUUUA 17 upstream (SEQ ID NO: 793) CEP290-B1072 − GAUUAUGUUACUUUUUA 17 upstream (SEQ ID NO: 793) CEP290-B1073 + GCAAAACAACUGGAAGA 17 downstream (SEQ ID NO: 794) CEP290-B1074 + GCAGAACUAGUGUAGAC 17 downstream (SEQ ID NO: 458) CEP290-B1075 − GCUCUUUUCUAUAUAUA 17 downstream (SEQ ID NO: 481) CEP290-B1076 + GGAUAGGACAGAGGACA 17 upstream (SEQ ID NO: 488) CEP290-B1077 + GGAUGUAAGACUGGAGA 17 downstream (SEQ ID NO: 795) CEP290-B1078 + GUAAGGAGGAUGUAAGA 17 downstream (SEQ ID NO: 796) CEP290-B1079 − GUAUCUCCUGUUUGGCA 17 downstream (SEQ ID NO: 797) CEP290-B1080 − GUCAUCUAGAGCAAGAG 17 downstream (SEQ ID NO: 798) CEP290-B1081 + GUCCUCAGUAAAAGGUA 17 upstream (SEQ ID NO: 799) CEP290-B1082 + GUGAAAGGAUCUUAGAU 17 upstream (SEQ ID NO: 800) CEP290-B1083 − GUGCUCUUUUCUAUAUA 17 downstream (SEQ ID NO: 801) CEP290-B1084 − GUGUCAAAUAUGGUGCU 17 downstream (SEQ ID NO: 802) CEP290-B1085 + GUUCCCUAUAUAUAGAA 17 downstream (SEQ ID NO: 803)

Table 5D provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the fourth tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 5D Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B1086 + AAAACUAAGACACUGCCAAU 20 downstream (SEQ ID NO: 610) CEP290-B1087 + AAAAGACUUAUAUUCCAUUA 20 downstream (SEQ ID NO: 685) CEP290-B1088 + AAACAUGACUCAUAAUUUAG 20 upstream (SEQ ID NO: 805) CEP290-B1089 + AAACAUGACUCAUAAUUUAG 20 upstream (SEQ ID NO: 805) CEP290-B1090 + AAAGAUGAAAAAUACUCUUU 20 upstream (SEQ ID NO: 737) CEP290-B1091 + AAAUUCACUGAGCAAAACAA 20 downstream (SEQ ID NO: 808) CEP290-B1092 + AACAAGUUUUGAAACAGGAA 20 downstream (SEQ ID NO: 809) CEP290-B1093 + AACAGGAGAUACUCAACACA 20 downstream (SEQ ID NO: 810) CEP290-B1094 + AACAUGACUCAUAAUUUAGU 20 upstream (SEQ ID NO: 721) CEP290-B1095 + AACAUGACUCAUAAUUUAGU 20 upstream (SEQ ID NO: 721) CEP290-B1096 − AAUAUAAGUCUUUUGAUAUA 20 downstream (SEQ ID NO: 687) CEP290-B1097 + AAUCACUCUCAUGUAUUAGC 20 downstream (SEQ ID NO: 814) CEP290-B1098 + AAUUCACUGAGCAAAACAAC 20 downstream (SEQ ID NO: 678) CEP290-B1099 + ACAAAAGAACAUACAUAAGA 20 downstream (SEQ ID NO: 816) CEP290-B1100 + ACGUACAAAAGAACAUACAU 20 downstream (SEQ ID NO: 817) CEP290-B1101 − ACGUGCUCUUUUCUAUAUAU 20 downstream (SEQ ID NO: 622) CEP290-B1102 − ACGUUGUUCUGAGUAGCUUU 20 upstream (SEQ ID NO: 749) CEP290-B1103 + ACUGAGCAAAACAACUGGAA 20 downstream (SEQ ID NO: 819) CEP290-B1104 + AGAGGAUAGGACAGAGGACA 20 upstream (SEQ ID NO: 735) CEP290-B1105 + AGAUGCAGAACUAGUGUAGA 20 downstream (SEQ ID NO: 821) CEP290-B1106 + AGCAAAAGCUUUUGAGCUAA 20 upstream (SEQ ID NO: 763) CEP290-B1107 − AGCAUUAGAAAGUCCUAGGC 20 upstream (SEQ ID NO: 823) CEP290-B1108 + AGCUUGAACUCUGUGCCAAA 20 downstream (SEQ ID NO: 824) CEP290-B1109 + AGCUUUUGACAGUUUUUAAG 20 downstream (SEQ ID NO: 825) CEP290-B1110 + AGGACAGAGGACAUGGAGAA 20 upstream (SEQ ID NO: 736) CEP290-B1111 + AGGAUAGGACAGAGGACAUG 20 upstream (SEQ ID NO: 827) CEP290-B1112 + AGGUAAUGCCUGAACAAGUU 20 downstream (SEQ ID NO: 828) CEP290-B1113 + AUAAGAAAGAACACUGUGGU 20 downstream (SEQ ID NO: 829) CEP290-B1114 + AUAAGCCUCUAUUUCUGAUG 20 upstream (SEQ ID NO: 723) CEP290-B1115 − AUACAUGAGAGUGAUUAGUG 20 downstream (SEQ ID NO: 831) CEP290-B1116 + AUAGAAAAGAGCACGUACAA 20 downstream (SEQ ID NO: 832) CEP290-B1117 + AUCAUUCUUGUGGCAGUAAG 20 downstream (SEQ ID NO: 833) CEP290-B1118 + AUCUUAUUCUACUCCUGUGA 20 upstream (SEQ ID NO: 764) CEP290-B1119 − AUCUUGUGGAUAAUGUAUCA 20 upstream (SEQ ID NO: 835) CEP290-B1120 + AUGAGGAAGAUGAACAAAUC 20 upstream (SEQ ID NO: 733) CEP290-B1121 + AUGAUCAUUCUUGUGGCAGU 20 downstream (SEQ ID NO: 837) CEP290-B1122 + AUGCUGGAGAGGAUAGGACA 20 upstream (SEQ ID NO: 838) CEP290-B1123 + AUGGUUCCCUAUAUAUAGAA 20 downstream (SEQ ID NO: 839) CEP290-B1124 − AUUUAAUUUGUUUCUGUGUG 20 downstream (SEQ ID NO: 840) CEP290-B1125 + CAAAACCUAUGUAUAAGAUG 20 downstream (SEQ ID NO: 841) CEP290-B1126 + CAAAAGACUUAUAUUCCAUU 20 downstream (SEQ ID NO: 842) CEP290-B1127 − CAAAAGCUUUUGCUGGCUCA 20 upstream (SEQ ID NO: 762) CEP290-B1128 − CAAGAAUGAUCAUUCUAAAC 20 downstream (SEQ ID NO: 844) CEP290-B1129 − CACAGAGUUCAAGCUAAUAC 20 downstream (SEQ ID NO: 845) CEP290-B1130 + CACAGGGUAGGAUUCAUGUU 20 downstream (SEQ ID NO: 846) CEP290-B1131 + CACUGCCAAUAGGGAUAGGU 20 downstream (SEQ ID NO: 613) CEP290-B1132 + CAGAACAACGUUUUCAUUUA 20 upstream (SEQ ID NO: 761) CEP290-B1133 − CAGAGUUCAAGCUAAUACAU 20 downstream (SEQ ID NO: 848) CEP290-B1134 − CAGUAAAUGAAAACGUUGUU 20 upstream (SEQ ID NO: 849) CEP290-B1135 − CAGUAAAUGAAAACGUUGUU 20 upstream (SEQ ID NO: 849) CEP290-B1136 + CAGUAAGGAGGAUGUAAGAC 20 downstream (SEQ ID NO: 676) CEP290-B1137 + CAUAAGCCUCUAUUUCUGAU 20 upstream (SEQ ID NO: 851) CEP290-B1138 − CAUAGAGACACAUUCAGUAA 20 upstream (SEQ ID NO: 750) CEP290-B1139 + CAUCUCUUGCUCUAGAUGAC 20 downstream (SEQ ID NO: 853) CEP290-B1140 − CAUGAGAGUGAUUAGUGGUG 20 downstream (SEQ ID NO: 854) CEP290-B1141 − CAUGUCAUCUAGAGCAAGAG 20 downstream (SEQ ID NO: 855) CEP290-B1142 + CAUUUACUGAAUGUGUCUCU 20 upstream (SEQ ID NO: 856) CEP290-B1143 + CAUUUACUGAAUGUGUCUCU 20 upstream (SEQ ID NO: 856) CEP290-B1144 + CCAUUAAAAAAAGUAUGCUU 20 downstream (SEQ ID NO: 857) CEP290-B1145 + CCUAGGACUUUCUAAUGCUG 20 upstream (SEQ ID NO: 858) CEP290-B1146 + CCUCUCUUUGGCAAAAGCAG 20 upstream (SEQ ID NO: 859) CEP290-B1147 + CCUCUCUUUGGCAAAAGCAG 20 upstream (SEQ ID NO: 859) CEP290-B1148 + CCUGUGAAAGGAUCUUAGAU 20 upstream (SEQ ID NO: 860) CEP290-B1149 − CGUGCUCUUUUCUAUAUAUA 20 downstream (SEQ ID NO: 624) CEP290-B1150 − CUAAGAUCCUUUCACAGGAG 20 upstream (SEQ ID NO: 861) CEP290-B1151 + CUAGAUGACAUGAGGUAAGU 20 downstream (SEQ ID NO: 671) CEP290-B1152 + CUAUGAGCCAGCAAAAGCUU 20 upstream (SEQ ID NO: 748) CEP290-B1153 + CUCAUAAUUUAGUAGGAAUC 20 upstream (SEQ ID NO: 864) CEP290-B1154 + CUCAUAAUUUAGUAGGAAUC 20 upstream (SEQ ID NO: 864) CEP290-B1155 − CUCAUCAGAAAUAGAGGCUU 20 upstream (SEQ ID NO: 865) CEP290-B1156 + CUCUAUUUCUGAUGAGGAAG 20 upstream (SEQ ID NO: 866) CEP290-B1157 − CUUAAGCAUACUUUUUUUAA 20 downstream (SEQ ID NO: 690) CEP290-B1158 − CUUAUCUAAGAUCCUUUCAC 20 upstream (SEQ ID NO: 734) CEP290-B1159 + CUUUCUAAUGCUGGAGAGGA 20 upstream (SEQ ID NO: 869) CEP290-B1160 + CUUUUGACAGUUUUUAAGGC 20 downstream (SEQ ID NO: 684) CEP290-B1161 + UAAAACUAAGACACUGCCAA 20 downstream (SEQ ID NO: 871) CEP290-B1162 + UAAGAAAAAAAAGGUAAUGC 20 downstream (SEQ ID NO: 872) CEP290-B1163 + UAAUGCUGGAGAGGAUAGGA 20 upstream (SEQ ID NO: 873) CEP290-B1164 − UACAUAUCUGUCUUCCUUAA 20 downstream (SEQ ID NO: 689) CEP290-B1165 − UACAUCCUCCUUACUGCCAC 20 downstream (SEQ ID NO: 875) CEP290-B1166 − UACAUGAGAGUGAUUAGUGG 20 downstream (SEQ ID NO: 628) CEP290-B1167 − UACCUCAUGUCAUCUAGAGC 20 downstream (SEQ ID NO: 876) CEP290-B1168 − UACGUGCUCUUUUCUAUAUA 20 downstream (SEQ ID NO: 877) CEP290-B1169 − UAGAGCAAGAGAUGAACUAG 20 downstream (SEQ ID NO: 878) CEP290-B1170 + UAGAUGACAUGAGGUAAGUA 20 downstream (SEQ ID NO: 680) CEP290-B1171 + UAGGAAUCCUGAAAGCUACU 20 upstream (SEQ ID NO: 760) CEP290-B1172 + UAGGACAGAGGACAUGGAGA 20 upstream (SEQ ID NO: 881) CEP290-B1173 + UAGGACUUUCUAAUGCUGGA 20 upstream (SEQ ID NO: 882) CEP290-B1174 + UCACUGAGCAAAACAACUGG 20 downstream (SEQ ID NO: 883) CEP290-B1175 − UCAUGUUUAUCAAUAUUAUU 20 upstream (SEQ ID NO: 884) CEP290-B1176 − UCAUGUUUAUCAAUAUUAUU 20 upstream (SEQ ID NO: 884) CEP290-B1177 + UCCACAAGAUGUCUCUUGCC 20 upstream (SEQ ID NO: 885) CEP290-B1178 + UCCAUAAGCCUCUAUUUCUG 20 upstream (SEQ ID NO: 886) CEP290-B1179 − UCCUAGGCAAGAGACAUCUU 20 upstream (SEQ ID NO: 887) CEP290-B1180 + UCUAGAUGACAUGAGGUAAG 20 downstream (SEQ ID NO: 888) CEP290-B1181 − UCUAUACCUUUUACUGAGGA 20 upstream (SEQ ID NO: 889) CEP290-B1182 + UCUGUCCUCAGUAAAAGGUA 20 upstream (SEQ ID NO: 890) CEP290-B1183 − UCUUAAGCAUACUUUUUUUA 20 downstream (SEQ ID NO: 891) CEP290-B1184 − UCUUAUCUAAGAUCCUUUCA 20 upstream (SEQ ID NO: 892) CEP290-B1185 − UCUUCCAGUUGUUUUGCUCA 20 downstream (SEQ ID NO: 893) CEP290-B1186 + UGAGCAAAACAACUGGAAGA 20 downstream (SEQ ID NO: 894) CEP290-B1187 − UGAGUAUCUCCUGUUUGGCA 20 downstream (SEQ ID NO: 895) CEP290-B1188 + UGAUCAUUCUUGUGGCAGUA 20 downstream (SEQ ID NO: 688) CEP290-B1189 + UGCCUAGGACUUUCUAAUGC 20 upstream (SEQ ID NO: 632) CEP290-B1190 + UGCCUGAACAAGUUUUGAAA 20 downstream (SEQ ID NO: 897) CEP290-B1191 − UGGUGUCAAAUAUGGUGCUU 20 downstream (SEQ ID NO: 625) CEP290-B1192 + UGUAAGACUGGAGAUAGAGA 20 downstream (SEQ ID NO: 898) CEP290-B1193 − UGUCCUAUCCUCUCCAGCAU 20 upstream (SEQ ID NO: 899) A CEP290-B1194 − UUAACGUUAUCAUUUUCCC 20 upstream (SEQ ID NO: 900) CEP290-B1195 − UUACAUAUCUGUCUUCCUUA 20 downstream (SEQ ID NO: 901) CEP290-B1196 + UUAGAUCUUAUUCUACUCCU 20 upstream (SEQ ID NO: 902) CEP290-B1197 + UUAGAUCUUAUUCUACUCCU 20 upstream (SEQ ID NO: 902) CEP290-B1198 − UUCAGGAUUCCUACUAAAUU 20 upstream (SEQ ID NO: 904) CEP290-B1199 − UUCAGGAUUCCUACUAAAUU 20 upstream (SEQ ID NO: 904) CEP290-B1200 − UUCAUCUUCCUCAUCAGAAA 20 upstream (SEQ ID NO: 905) CEP290-B1201 + UUGCCUAGGACUUUCUAAUG 20 upstream (SEQ ID NO: 906) CEP290-B1202 − UUUCUGCUGCUUUUGCCAAA 20 upstream (SEQ ID NO: 907) CEP290-B1203 − UUUCUGCUGCUUUUGCCAAA 20 upstream (SEQ ID NO: 907) CEP290-B1204 + UUUUGACAGUUUUUAAGGCG 20 downstream (SEQ ID NO: 681) CEP290-B1205 + UUUUUAAGGCGGGGAGUCAC 20 downstream (SEQ ID NO: 909) CEP290-B1206 + AAAAGCUUUUGAGCUAA 17 upstream (SEQ ID NO: 767) CEP290-B1207 + AAAGAACAUACAUAAGA 17 downstream (SEQ ID NO: 911) CEP290-B1208 + AAAUGGUUCCCUAUAUA 17 downstream (SEQ ID NO: 912) CEP290-B1209 + AACAACGUUUUCAUUUA 17 upstream (SEQ ID NO: 765) CEP290-B1210 + AACCUAUGUAUAAGAUG 17 downstream (SEQ ID NO: 914) CEP290-B1211 + AACUAAGACACUGCCAA 17 downstream (SEQ ID NO: 915) CEP290-B1212 + AAGACUGGAGAUAGAGA 17 downstream (SEQ ID NO: 916) CEP290-B1213 + AAGACUUAUAUUCCAUU 17 downstream (SEQ ID NO: 917) CEP290-B1214 + AAGAUGAAAAAUACUCU 17 upstream (SEQ ID NO: 918) CEP290-B1215 − AAGCAUACUUUUUUUAA 17 downstream (SEQ ID NO: 667) CEP290-B1216 + AAGCCUCUAUUUCUGAU 17 upstream (SEQ ID NO: 920) CEP290-B1217 − AAGCUUUUGCUGGCUCA 17 upstream (SEQ ID NO: 766) CEP290-B1218 + AAGUUUUGAAACAGGAA 17 downstream (SEQ ID NO: 922) CEP290-B1219 + ACAAGAUGUCUCUUGCC 17 upstream (SEQ ID NO: 923) CEP290-B1220 + ACAGAGGACAUGGAGAA 17 upstream (SEQ ID NO: 715) CEP290-B1221 + ACAGGAAUAGAAAUUCA 17 downstream (SEQ ID NO: 925) CEP290-B1222 + ACAUGGGAGUCACAGGG 17 downstream (SEQ ID NO: 926) CEP290-B1223 − ACGUUAUCAUUUUCCCA 17 upstream (SEQ ID NO: 927) CEP290-B1224 + ACUAAGACACUGCCAAU 17 downstream (SEQ ID NO: 603) CEP290-B1225 + AGAAAGAACACUGUGGU 17 downstream (SEQ ID NO: 928) CEP290-B1226 + AGACUGGAGAUAGAGAC 17 downstream (SEQ ID NO: 664) CEP290-B1227 + AGACUUAUAUUCCAUUA 17 downstream (SEQ ID NO: 651) CEP290-B1228 − AGAGACACAUUCAGUAA 17 upstream (SEQ ID NO: 754) CEP290-B1229 − AGAGUUCAAGCUAAUAC 17 downstream (SEQ ID NO: 931) CEP290-B1230 − AGAUCCUUUCACAGGAG 17 upstream (SEQ ID NO: 932) CEP290-B1231 + AGAUGAAAAAUACUCUU 17 upstream (SEQ ID NO: 718) CEP290-B1232 + AGAUGACAUGAGGUAAG 17 downstream (SEQ ID NO: 934) CEP290-B1233 − AGCAAGAGAUGAACUAG 17 downstream (SEQ ID NO: 935) CEP290-B1234 + AGCCUCUAUUUCUGAUG 17 upstream (SEQ ID NO: 709) CEP290-B1235 + AGGAAGAUGAACAAAUC 17 upstream (SEQ ID NO: 717) CEP290-B1236 + AGGACUUUCUAAUGCUG 17 upstream (SEQ ID NO: 938) CEP290-B1237 + AGGAGAUACUCAACACA 17 downstream (SEQ ID NO: 939) CEP290-B1238 + AGGAUAGGACAGAGGAC 17 upstream (SEQ ID NO: 940) CEP290-B1239 − AGGAUUCCUACUAAAUU 17 upstream (SEQ ID NO: 941) CEP290-B1240 − AGGAUUCCUACUAAAUU 17 upstream (SEQ ID NO: 941) CEP290-B1241 + AGGGUAGGAUUCAUGUU 17 downstream (SEQ ID NO: 942) CEP290-B1242 − AGUUCAAGCUAAUACAU 17 downstream (SEQ ID NO: 943) CEP290-B1243 + AUAAGCCUCUAUUUCUG 17 upstream (SEQ ID NO: 944) CEP290-B1244 − AUAAGUCUUUUGAUAUA 17 downstream (SEQ ID NO: 661) CEP290-B1245 + AUAAUUUAGUAGGAAUC 17 upstream (SEQ ID NO: 946) CEP290-B1246 + AUAAUUUAGUAGGAAUC 17 upstream (SEQ ID NO: 946) CEP290-B1247 − AUACCUUUUACUGAGGA 17 upstream (SEQ ID NO: 947) CEP290-B1248 − AUAGAGGCUUAUGGAUU 17 upstream (SEQ ID NO: 948) CEP290-B1249 + AUAGGACAGAGGACAUG 17 upstream (SEQ ID NO: 949) CEP290-B1250 − AUAUCUGUCUUCCUUAA 17 downstream (SEQ ID NO: 658) CEP290-B1251 − AUCAGAAAUAGAGGCUU 17 upstream (SEQ ID NO: 951) CEP290-B1252 + AUCAUUCUUGUGGCAGU 17 downstream (SEQ ID NO: 952) CEP290-B1253 − AUCCUCCUUACUGCCAC 17 downstream (SEQ ID NO: 953) CEP290-B1254 − AUCUAAGAUCCUUUCAC 17 upstream (SEQ ID NO: 696) CEP290-B1255 − AUCUUCCUCAUCAGAAA 17 upstream (SEQ ID NO: 955) CEP290-B1256 + AUGACAUGAGGUAAGUA 17 downstream (SEQ ID NO: 656) CEP290-B1257 + AUGACUCAUAAUUUAGU 17 upstream (SEQ ID NO: 704) CEP290-B1258 + AUGACUCAUAAUUUAGU 17 upstream (SEQ ID NO: 704) CEP290-B1259 − AUGAGAGUGAUUAGUGG 17 downstream (SEQ ID NO: 645) CEP290-B1260 − AUUAGAAAGUCCUAGGC 17 upstream (SEQ ID NO: 957) CEP290-B1261 + AUUCUUGUGGCAGUAAG 17 downstream (SEQ ID NO: 958) CEP290-B1262 + CACUCUCAUGUAUUAGC 17 downstream (SEQ ID NO: 959) CEP290-B1263 − CAUAUCUGUCUUCCUUA 17 downstream (SEQ ID NO: 960) CEP290-B1264 + CAUGACUCAUAAUUUAG 17 upstream (SEQ ID NO: 961) CEP290-B1265 + CAUGACUCAUAAUUUAG 17 upstream (SEQ ID NO: 961) CEP290-B1266 − CAUGAGAGUGAUUAGUG 17 downstream (SEQ ID NO: 962) CEP290-B1267 + CCUAGGACUUUCUAAUG 17 upstream (SEQ ID NO: 963) CEP290-B1268 − CCUAUCCUCUCCAGCAU 17 upstream (SEQ ID NO: 964) CEP290-B1269 + CUAGGACUUUCUAAUGC 17 upstream (SEQ ID NO: 695) CEP290-B1270 − CUCAUGUCAUCUAGAGC 17 downstream (SEQ ID NO: 966) CEP290-B1271 + CUCUUGCUCUAGAUGAC 17 downstream (SEQ ID NO: 967) CEP290-B1272 + CUCUUUGGCAAAAGCAG 17 upstream (SEQ ID NO: 968) CEP290-B1273 + CUCUUUGGCAAAAGCAG 17 upstream (SEQ ID NO: 968) CEP290-B1274 + CUGAACAAGUUUUGAAA 17 downstream (SEQ ID NO: 970) CEP290-B1275 + CUGAGCAAAACAACUGG 17 downstream (SEQ ID NO: 971) CEP290-B1276 − CUGCUGCUUUUGCCAAA 17 upstream (SEQ ID NO: 972) CEP290-B1277 − CUGCUGCUUUUGCCAAA 17 upstream (SEQ ID NO: 972) CEP290-B1278 + CUGGAGAGGAUAGGACA 17 upstream (SEQ ID NO: 973) CEP290-B1279 − UAAAUGAAAACGUUGUU 17 upstream (SEQ ID NO: 974) CEP290-B1280 − UAAAUGAAAACGUUGUU 17 upstream (SEQ ID NO: 974) CEP290-B1281 − UAAGCAUACUUUUUUUA 17 downstream (SEQ ID NO: 975) CEP290-B1282 + UAAGGAGGAUGUAAGAC 17 downstream (SEQ ID NO: 648) CEP290-B1283 + UAAUGCCUGAACAAGUU 17 downstream (SEQ ID NO: 976) CEP290-B1284 − UAAUUUGUUUCUGUGUG 17 downstream (SEQ ID NO: 977) CEP290-B1285 + UACAAAAGAACAUACAU 17 downstream (SEQ ID NO: 978) CEP290-B1286 − UAGGCAAGAGACAUCUU 17 upstream (SEQ ID NO: 979) CEP290-B1287 − UAUAAGUCUUUUGAUAU 17 downstream (SEQ ID NO: 980) CEP290-B1288 − UAUCUAAGAUCCUUUCA 17 upstream (SEQ ID NO: 981) CEP290-B1289 + UAUUUCUGAUGAGGAAG 17 upstream (SEQ ID NO: 982) CEP290-B1290 + UCACUGAGCAAAACAAC 17 downstream (SEQ ID NO: 650) CEP290-B1291 + UCAUUCUUGUGGCAGUA 17 downstream (SEQ ID NO: 2780) CEP290-B1292 − UCCAGUUGUUUUGCUCA 17 downstream (SEQ ID NO: 983) CEP290-B1293 + UCUAAUGCUGGAGAGGA 17 upstream (SEQ ID NO: 984) CEP290-B1294 + UGAACAAGUUUUGAAAC 17 downstream (SEQ ID NO: 659) CEP290-B1295 + UGAACUCUGUGCCAAAC 17 downstream (SEQ ID NO: 638) CEP290-B1296 + UGACAGUUUUUAAGGCG 17 downstream (SEQ ID NO: 642) CEP290-B1297 + UGAGCCAGCAAAAGCUU 17 upstream (SEQ ID NO: 752) CEP290-B1298 + UGCAGAACUAGUGUAGA 17 downstream (SEQ ID NO: 987) CEP290-B1299 + UGCCAAUAGGGAUAGGU 17 downstream (SEQ ID NO: 614) CEP290-B1300 − UGCUCUUUUCUAUAUAU 17 downstream (SEQ ID NO: 663) CEP290-B1301 + UGCUGGAGAGGAUAGGA 17 upstream (SEQ ID NO: 989) CEP290-B1302 − UGUCAAAUAUGGUGCUU 17 downstream (SEQ ID NO: 643) CEP290-B1303 − UGUUUAUCAAUAUUAUU 17 upstream (SEQ ID NO: 990) CEP290-B1304 − UGUUUAUCAAUAUUAUU 17 upstream (SEQ ID NO: 990) CEP290-B1305 + UUAAAAAAAGUAUGCUU 17 downstream (SEQ ID NO: 991) CEP290-B1306 + UUAAGGCGGGGAGUCAC 17 downstream (SEQ ID NO: 992) CEP290-B1307 + UUACUGAAUGUGUCUCU 17 upstream (SEQ ID NO: 993) CEP290-B1308 + UUACUGAAUGUGUCUCU 17 upstream (SEQ ID NO: 993) CEP290-B1309 + UUAUUCUACUCCUGUGA 17 upstream (SEQ ID NO: 768) CEP290-B1310 + UUCACUGAGCAAAACAA 17 downstream (SEQ ID NO: 995) CEP290-B1311 − UUCUGCUGCUUUUGCCA 17 upstream (SEQ ID NO: 996) CEP290-B1312 − UUCUGCUGCUUUUGCCA 17 upstream (SEQ ID NO: 996) CEP290-B1313 + UUGAACUCUGUGCCAAA 17 downstream (SEQ ID NO: 997) CEP290-B1314 + UUGACAGUUUUUAAGGC 17 downstream (SEQ ID NO: 654) CEP290-B1315 − UUGUGGAUAAUGUAUCA 17 upstream (SEQ ID NO: 999) CEP290-B1316 − UUGUUCAUCUUCCUCAU 17 upstream (SEQ ID NO: 1000) CEP290-B1317 − UUGUUCUGAGUAGCUUU 17 upstream (SEQ ID NO: 753) CEP290-B1318 + UUUGACAGUUUUUAAGG 17 downstream (SEQ ID NO: 662) CEP290-B1319 + UUUUGACAGUUUUUAAG 17 downstream (SEQ ID NO: 1003)

Table 6A provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, have good orthogonality, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a N. meningitidis Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 6A  Target Position relative gRNA  DNA Site to Name Strand Targeting Domain Length mutation CEP290- − GAGUUCAAGCUAAUACAUGA 20 downstream B65 (SEQ ID NO: 589) CEP290- − GUUGUUCUGAGUAGCUU 17 upstream B296 (SEQ ID NO: 590) CEP290- + GGCAAAAGCAGCAGAAAGCA 20 upstream B308 (SEQ ID NO: 591) CEP290- − GUUGUUCUGAGUAGCUU 17 upstream B536 (SEQ ID NO: 590) CEP290- + GGCAAAAGCAGCAGAAAGCA 20 upstream B482 (SEQ ID NO: 591)

Table 6B provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 400 bp upstream of an Alu repeat or 700 bp downstream of the mutation, have good orthogonality, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a N. meningitidis Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 6B  Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-B235 − UUCAAGCUAAUACAUGA 17 downstream (SEQ ID NO: 1004) CEP290-B109 + CACAUGGGAGUCACAGG 17 downstream (SEQ ID NO: 1005) CEP290-B129 + AGUCACAUGGGAGUCACAGG 20 downstream (SEQ ID NO: 1006) CEP290-B295 − AAUAGAGGCUUAUGGAU 17 upstream (SEQ ID NO: 1007) CEP290-B297 − CUGAGGACAGAACAAGC 17 upstream (SEQ ID NO: 1008) CEP290-B298 − CAUCAGAAAUAGAGGCU 17 upstream (SEQ ID NO: 1009) CEP290-B299 − CUGCUUUUGCCAAAGAG 17 upstream (SEQ ID NO: 711) CEP290-B300 + AGCAGAAAGCAAACUGA 17 upstream (SEQ ID NO: 1011) CEP290-B301 + AAAAGCAGCAGAAAGCA 17 upstream (SEQ ID NO: 1012) CEP290-B302 − UUACUGAGGACAGAACAAGC 20 upstream (SEQ ID NO: 1013) CEP290-B303 − AACGUUGUUCUGAGUAGCUU 20 upstream (SEQ ID NO: 1014) CEP290-B304 − CUGCUGCUUUUGCCAAAGAG 20 upstream (SEQ ID NO: 725) CEP290-B305 − AGAAAUAGAGGCUUAUGGAU 20 upstream (SEQ ID NO: 1016) CEP290-B306 − CCUCAUCAGAAAUAGAGGCU 20 upstream (SEQ ID NO: 1017) CEP290-B307 + AGCAGCAGAAAGCAAACUGA 20 upstream (SEQ ID NO: 1018) CEP290-B531 − CUGCUUUUGCCAAAGAG 17 upstream (SEQ ID NO: 711) CEP290-B522 + AGCAGAAAGCAAACUGA 17 upstream (SEQ ID NO: 1011) CEP290-B537 + AAAAGCAGCAGAAAGCA 17 upstream (SEQ ID NO: 1012) CEP290-B504 − AACGUUGUUCUGAGUAGCUU 20 upstream (SEQ ID NO: 1014) CEP290-B478 − CUGCUGCUUUUGCCAAAGAG 20 upstream (SEQ ID NO: 725) CEP290-B526 + AGCAGCAGAAAGCAAACUGA 20 upstream (SEQ ID NO: 1018)

Table 7A provides targeting domains for introduction of an indel (e.g., mediated by NHEJ) in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 40 bases of the LCA10 target position, have good orthogonality, start with G and PAM is NNGRRT. It is contemplated herein that in an embodiment the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 7A DNA Targeting Domain Target gRNA Name Strand Length Site CEP290-12 − GCACCUGGCCCCAGUUGUAAUU 22 (SEQ ID NO: 398)

Table 7B provides targeting domains for introduction of an indel (e.g., mediated by NHEJ) in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 40 bases of the LCA10 target position, have good orthogonality, and PAM is NNGRRT. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 7B Target DNA Site gRNA Name Strand Targeting Domain Length CEP290-35 + AAAUAAAACUAAGACACUGCCAAU 24 (SEQ ID NO: 1025) CEP290-36 + AAUAAAACUAAGACACUGCCAAU 23 (SEQ ID NO: 1026) CEP290-37 + AUAAAACUAAGACACUGCCAAU 22 (SEQ ID NO: 1027) CEP290-38 + AAAACUAAGACACUGCCAAU  20 (SEQ ID NO: 610) CEP290-39 + AAACUAAGACACUGCCAAU  19 (SEQ ID NO: 1028) CEP290-40 + AACUAAGACACUGCCAAU  18 (SEQ ID NO: 1029) CEP290-512 − ACCUGGCCCCAGUUGUAAUU  20 (SEQ ID NO: 616) CEP290-17 − CCGCACCUGGCCCCAGUUGUAAUU 24 (SEQ ID NO: 1030) CEP290-41 − CGCACCUGGCCCCAGUUGUAAUU 23 (SEQ ID NO: 1031) CEP290-42 − CACCUGGCCCCAGUUGUAAUU 21 (SEQ ID NO: 1032) CEP290-513 − CCUGGCCCCAGUUGUAAUU  19 (SEQ ID NO: 1033) CEP290-514 − CUGGCCCCAGUUGUAAUU  18 (SEQ ID NO: 1034) CEP290-43 + UAAAACUAAGACACUGCCAAU 21 (SEQ ID NO: 1035)

Table 7C provides targeting domains for introduction of an indel (e.g., mediated by NHEJ) in close proximity to or including the LCA10 target position in the CEP290 gene selected according to the fifth tier parameters. The targeting domains are within 40 bases of the LCA10 target position, and PAM is NNGRRV. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 7C Target DNA Site gRNA Name Strand Targeting Domain Length CEP290-44 + AAAAUAAAACUAAGACACUGCCAA 24 (SEQ ID NO: 1036) CEP290-45 + AAAUAAAACUAAGACACUGCCAA 23 (SEQ ID NO: 1037) CEP290-46 + AAUAAAACUAAGACACUGCCAA 22 (SEQ ID NO: 1038) CEP290-47 + AUAAAACUAAGACACUGCCAA 21 (SEQ ID NO: 1039) CEP290-48 + AAAACUAAGACACUGCCAA 19 (SEQ ID NO: 1040) CEP290-49 + AAACUAAGACACUGCCAA 18 (SEQ ID NO: 1041) CEP290-16 + AAGACACUGCCAAUAGGGAUAGGU 24 (SEQ ID NO: 1042) CEP290-50 + AGACACUGCCAAUAGGGAUAGGU 23 (SEQ ID NO: 1043) CEP290-51 + ACACUGCCAAUAGGGAUAGGU 21 (SEQ ID NO: 1044) CEP290-510 + ACUGCCAAUAGGGAUAGGU 19 (SEQ ID NO: 1045) CEP290-509 + CACUGCCAAUAGGGAUAGGU 20 (SEQ ID NO: 613) CEP290-511 + CUGCCAAUAGGGAUAGGU 18 (SEQ ID NO: 1046) CEP290-11 + GACACUGCCAAUAGGGAUAGGU 22 (SEQ ID NO: 1047) CEP290-52 + UAAAACUAAGACACUGCCAA 20 (SEQ ID NO: 871) CEP290-13 + AUGAGAUACUCACAAUUACAAC 22 (SEQ ID NO: 1049) CEP290-53 + AGAUACUCACAAUUACAAC 19 (SEQ ID NO: 1050) CEP290-18 + GUAUGAGAUACUCACAAUUACAAC 24 (SEQ ID NO: 1051) CEP290-54 + GAGAUACUCACAAUUACAAC 20 (SEQ ID NO: 395) CEP290-55 + GAUACUCACAAUUACAAC 18 (SEQ ID NO: 1052) CEP290-14 + UAUGAGAUACUCACAAUUACAAC 23 (SEQ ID NO: 1053) CEP290-57 + UGAGAUACUCACAAUUACAAC 21 (SEQ ID NO: 1054) CEP290-58 + AUGAGAUAUUCACAAUUACAA 21 (SEQ ID NO: 1055) CEP290-59 + AGAUAUUCACAAUUACAA 18 (SEQ ID NO: 1056) CEP290-19 + GGUAUGAGAUAUUCACAAUUACAA 24 (SEQ ID NO: 1057) CEP290-61 + GUAUGAGAUAUUCACAAUUACAA 23 (SEQ ID NO: 1058) CEP290-63 + GAGAUAUUCACAAUUACAA 19 (SEQ ID NO: 1059) CEP290-65 + UAUGAGAUAUUCACAAUUACAA 22 (SEQ ID NO: 1060) CEP290-66 + UGAGAUAUUCACAAUUACAA 20 (SEQ ID NO: 1061)

Table 7D provides targeting domains for introduction of an indel (e.g., mediated by NHEJ) in close proximity to or including the LCA10 target position in the CEP290 gene that can be used for dual targeting. Any of the targeting domains in the table can be used with a S. aureus Cas9 (nickase) molecule to generate a single stranded break. Exemplary nickase pairs including selecting a targeting domain from Group A and a second targeting domain from Group B. It is contemplated herein that a targeting domain of Group A can be combined with any of the targeting domains of Group B. For example, the CEP290-12 or CEP290-17 can be combined with CEP290-11 or CEP290-16.

TABLE 7D Group A Group B CEP290-12 CEP290-11 CEP290-17 CEP290-16

Table 8A provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, have good orthogonality, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 8A  Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-67 + GAAAGAUGAAAAAUACUCUU 20 upstream (SEQ ID NO: 462) CEP290-68 − GAAAUAGAUGUAGAUUG 17 downstream (SEQ ID NO: 463) CEP290-70 − GAAAUAUUAAGGGCUCUUCC 20 upstream (SEQ ID NO: 464) CEP290-71 + GAACAAAAGCCAGGGACCAU 20 upstream (SEQ ID NO: 465) CEP290-72 − GAACUCUAUACCUUUUACUG 20 upstream (SEQ ID NO: 466) CEP290-73 − GAAGAAUGGAAUAGAUAAUA 20 downstream (SEQ ID NO: 467) CEP290-74 + GAAUAGUUUGUUCUGGGUAC 20 upstream (SEQ ID NO: 468) CEP290-75 − GAAUGGAAUAGAUAAUA 17 downstream (SEQ ID NO: 469) CEP290-76 + GAAUUUACAGAGUGCAUCCA 20 upstream (SEQ ID NO: 470) CEP290-77 − GAGAAAAAGGAGCAUGAAAC 20 upstream (SEQ ID NO: 471) CEP290-78 − GAGAGCCACAGUGCAUG 17 downstream (SEQ ID NO: 472) CEP290-79 − GAGGUAGAAUCAAGAAG 17 downstream (SEQ ID NO: 473) CEP290-80 + GAGUGCAUCCAUGGUCC 17 upstream (SEQ ID NO: 474) CEP290-81 + GAUAACUACAAAGGGUC 17 upstream (SEQ ID NO: 475) CEP290-82 + GAUAGAGACAGGAAUAA 17 downstream (SEQ ID NO: 476) CEP290-83 + GAUGAAAAAUACUCUUU 17 upstream (SEQ ID NO: 477) CEP290-84 + GAUGACAUGAGGUAAGU 17 downstream (SEQ ID NO: 478) CEP290-85 + GAUGCAGAACUAGUGUAGAC 20 downstream (SEQ ID NO: 460) CEP290-86 + GCAGAACUAGUGUAGAC 17 downstream (SEQ ID NO: 458) CEP290-87 − GCAUGUGGUGUCAAAUA 17 downstream (SEQ ID NO: 479) CEP290-88 + GCCUGAACAAGUUUUGAAAC 20 downstream (SEQ ID NO: 480) CEP290-89 − GCUACCGGUUACCUGAA 17 downstream (SEQ ID NO: 457) CEP290-90 − GCUCUUUUCUAUAUAUA 17 downstream (SEQ ID NO: 481) CEP290-91 + GCUUGAACUCUGUGCCAAAC 20 downstream (SEQ ID NO: 461) CEP290-92 + GCUUUUGACAGUUUUUAAGG 20 downstream (SEQ ID NO: 482) CEP290-93 − GCUUUUGUUCCUUGGAA 17 upstream (SEQ ID NO: 483) CEP290-94 + GGAACAAAAGCCAGGGACCA 20 upstream (SEQ ID NO: 484) CEP290-95 + GGACUUGACUUUUACCCUUC 20 downstream (SEQ ID NO: 485) CEP290-96 + GGAGAAUAGUUUGUUCU 17 upstream (SEQ ID NO: 486) CEP290-97 + GGAGUCACAUGGGAGUCACA 20 downstream (SEQ ID NO: 487) CEP290-98 + GGAUAGGACAGAGGACA 17 upstream (SEQ ID NO: 488) CEP290-99 + GGCUGUAAGAUAACUACAAA 20 upstream (SEQ ID NO: 489) CEP290-100 + GGGAGAAUAGUUUGUUC 17 upstream (SEQ ID NO: 490) CEP290-101 + GGGAGUCACAUGGGAGUCAC 20 downstream (SEQ ID NO: 491) CEP290-102 − GGGCUCUUCCUGGACCA 17 upstream (SEQ ID NO: 492) CEP290-103 + GGGUACAGGGGUAAGAGAAA 20 upstream (SEQ ID NO: 493) CEP290-104 − GGUCCCUGGCUUUUGUUCCU 20 upstream (SEQ ID NO: 494) CEP290-105 − GUAAAGGUUCAUGAGACUAG 20 downstream (SEQ ID NO: 495) CEP290-106 + GUAACAUAAUCACCUCUCUU 20 upstream (SEQ ID NO: 496) CEP290-107 + GUAAGACUGGAGAUAGAGAC 20 downstream (SEQ ID NO: 497) CEP290-108 + GUACAGGGGUAAGAGAA 17 upstream (SEQ ID NO: 498) CEP290-109 + GUAGCUUUUGACAGUUUUUA 20 downstream (SEQ ID NO: 499) CEP290-110 + GUCACAUGGGAGUCACA 17 downstream (SEQ ID NO: 500) CEP290-111 − GUGGAGAGCCACAGUGCAUG 20 downstream (SEQ ID NO: 501) CEP290-112 − GUUACAAUCUGUGAAUA 17 upstream (SEQ ID NO: 502) CEP290-113 + GUUCUGUCCUCAGUAAA 17 upstream (SEQ ID NO: 503) CEP290-114 − GUUGAGUAUCUCCUGUU 17 downstream (SEQ ID NO: 459) CEP290-115 + GUUUAGAAUGAUCAUUCUUG 20 downstream (SEQ ID NO: 504) CEP290-116 + GUUUGUUCUGGGUACAG 17 upstream (SEQ ID NO: 505) CEP290-117 − UAAAAACUGUCAAAAGCUAC 20 downstream (SEQ ID NO: 506) CEP290-118 + UAAAAGGUAUAGAGUUCAAG 20 upstream (SEQ ID NO: 507) CEP290-119 + UAAAUCAUGCAAGUGACCUA 20 upstream (SEQ ID NO: 508) CEP290-120 + UAAGAUAACUACAAAGGGUC 20 upstream (SEQ ID NO: 509)

Table 8B provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, have good orthogonality, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 8B Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-121 − AAAAAGGAGCAUGAAAC 17 upstream (SEQ ID NO: 1062) CEP290-122 + AAAACUAAGACACUGCCAAU 20 downstream (SEQ ID NO: 610) CEP290-123 + AAAAGACUUAUAUUCCAUUA 20 downstream (SEQ ID NO: 685) CEP290-124 − AAAAGCUACCGGUUACCUGA 20 downstream (SEQ ID NO: 621) CEP290-125 − AAAAUUAUGCCUAUUUAGUG 20 upstream (SEQ ID NO: 729) CEP290-126 + AAACAACUGGAAGAGAGAAA 20 downstream (SEQ ID NO: 691) CEP290-127 + AAACUAAGACACUGCCAAUA 20 downstream (SEQ ID NO: 609) CEP290-128 − AAACUGUCAAAAGCUAC 17 downstream (SEQ ID NO: 655) CEP290-129 − AAAGAAAUAGAUGUAGAUUG 20 downstream (SEQ ID NO: 1066) CEP290-130 + AAAGAUGAAAAAUACUCUUU 20 upstream (SEQ ID NO: 737) CEP290-131 − AAAGCUACCGGUUACCUGAA 20 downstream (SEQ ID NO: 620) CEP290-133 − AAAUAGAGGCUUAUGGAUUU 20 upstream (SEQ ID NO: 731) CEP290-134 + AAAUUAUCACCACACUAAAU 20 upstream (SEQ ID NO: 727) CEP290-135 − AACAAACUAUUCUCCCA 17 upstream (SEQ ID NO: 1070) CEP290-136 − AACAGUAGCUGAAAUAUUAA 20 upstream (SEQ ID NO: 1071) CEP290-137 + AACAUGACUCAUAAUUUAGU 20 upstream (SEQ ID NO: 721) CEP290-138 − AACUAUUCUCCCAUGGUCCC 20 upstream (SEQ ID NO: 1073) CEP290-140 + AAGACACUGCCAAUAGGGAU 20 downstream (SEQ ID NO: 600) CEP290-141 − AAGGAAAUACAAAAACUGGA 20 downstream (SEQ ID NO: 1074) CEP290-142 + AAGGUAUAGAGUUCAAG 17 upstream (SEQ ID NO: 1075) CEP290-143 − AAGGUUCAUGAGACUAG 17 downstream (SEQ ID NO: 1076) CEP290-144 + AAUAGUUUGUUCUGGGUACA 20 upstream (SEQ ID NO: 1077) CEP290-145 − AAUAUAAGUCUUUUGAUAUA 20 downstream (SEQ ID NO: 687) CEP290-146 − AAUAUAUUAUCUAUUUAUAG 20 upstream (SEQ ID NO: 1079) CEP290-147 − AAUAUUGUAAUCAAAGG 17 upstream (SEQ ID NO: 1080) CEP290-148 + AAUAUUUCAGCUACUGU 17 upstream (SEQ ID NO: 1081) CEP290-149 − AAUUAUUGUUGCUUUUUGAG 20 downstream (SEQ ID NO: 1082) CEP290-150 + AAUUCACUGAGCAAAACAAC 20 downstream (SEQ ID NO: 678) CEP290-151 + ACAAAAGCCAGGGACCA 17 upstream (SEQ ID NO: 1084) CEP290-152 + ACACUGCCAAUAGGGAU 17 downstream (SEQ ID NO: 595) CEP290-153 + ACAGAGUGCAUCCAUGGUCC 20 upstream (SEQ ID NO: 1085) CEP290-154 + ACAUAAUCACCUCUCUU 17 upstream (SEQ ID NO: 712) CEP290-155 − ACCAGACAUCUAAGAGAAAA 20 upstream (SEQ ID NO: 1087) CEP290-156 − ACGUGCUCUUUUCUAUAUAU 20 downstream (SEQ ID NO: 622) CEP290-157 + ACUUUCUAAUGCUGGAG 17 upstream (SEQ ID NO: 700) CEP290-158 + ACUUUUACCCUUCAGGUAAC 20 downstream (SEQ ID NO: 626) CEP290-159 − AGAAUAUUGUAAUCAAAGGA 20 upstream (SEQ ID NO: 1089) CEP290-160 − AGACAUCUAAGAGAAAA 17 upstream (SEQ ID NO: 1090) CEP290-161 + AGACUUAUAUUCCAUUA 17 downstream (SEQ ID NO: 651) CEP290-162 + AGAGGAUAGGACAGAGGACA 20 upstream (SEQ ID NO: 735) CEP290-163 + AGAUGACAUGAGGUAAGUAG 20 downstream (SEQ ID NO: 677) CEP290-164 + AGAUGUCUGGUUAAAAG 17 upstream (SEQ ID NO: 1093) CEP290-165 + AGCCUCUAUUUCUGAUG 17 upstream (SEQ ID NO: 709) CEP290-166 − AGCUACCGGUUACCUGA 17 downstream (SEQ ID NO: 618) CEP290-167 − AGCUCAAAAGCUUUUGC 17 upstream (SEQ ID NO: 698) CEP290-168 − AGGAAAUACAAAAACUGGAU 20 downstream (SEQ ID NO: 1096) CEP290-169 + AGGAAGAUGAACAAAUC 17 upstream (SEQ ID NO: 717) CEP290-170 + AGGACAGAGGACAUGGAGAA 20 upstream (SEQ ID NO: 736) CEP290-171 + AGGACUUUCUAAUGCUGGAG 20 upstream (SEQ ID NO: 719) CEP290-172 − AGGCAAGAGACAUCUUG 17 upstream (SEQ ID NO: 708) CEP290-173 − AGGUAGAAUAUUGUAAUCAA 20 upstream (SEQ ID NO: 1101) CEP290-174 − AGUAGCUGAAAUAUUAA 17 upstream (SEQ ID NO: 1102) CEP290-175 + AGUCACAUGGGAGUCAC 17 downstream (SEQ ID NO: 644) CEP290-176 − AGUGCAUGUGGUGUCAAAUA 20 downstream (SEQ ID NO: 627) CEP290-177 + AGUUUGUUCUGGGUACA 17 upstream (SEQ ID NO: 1103) CEP290-178 + AUAAGCCUCUAUUUCUGAUG 20 upstream (SEQ ID NO: 723) CEP290-179 − AUAAGUCUUUUGAUAUA 17 downstream (SEQ ID NO: 661) CEP290-180 + AUACAUAAGAAAGAACACUG 20 downstream (SEQ ID NO: 686) CEP290-181 + AUAGUUUGUUCUGGGUACAG 20 upstream (SEQ ID NO: 1107) CEP290-182 − AUAUCUGUCUUCCUUAA 17 downstream (SEQ ID NO: 658) CEP290-183 − AUAUUAAGGGCUCUUCC 17 upstream (SEQ ID NO: 1109) CEP290-184 − AUAUUGUAAUCAAAGGA 17 upstream (SEQ ID NO: 1110) CEP290-185 + AUCAUGCAAGUGACCUA 17 upstream (SEQ ID NO: 1111) CEP290-186 − AUCUAAGAUCCUUUCAC 17 upstream (SEQ ID NO: 696) CEP290-187 − AUCUUCCUCAUCAGAAAUAG 20 upstream (SEQ ID NO: 722) CEP290-188 + AUGACAUGAGGUAAGUA 17 downstream (SEQ ID NO: 656) CEP290-189 + AUGACUCAUAAUUUAGU 17 upstream (SEQ ID NO: 704) CEP290-190 − AUGAGAGUGAUUAGUGG 17 downstream (SEQ ID NO: 645) CEP290-191 + AUGAGGAAGAUGAACAAAUC 20 upstream (SEQ ID NO: 733) CEP290-192 + AUGGGAGAAUAGUUUGUUCU 20 upstream (SEQ ID NO: 1116) CEP290-193 − AUUAGCUCAAAAGCUUUUGC 20 upstream (SEQ ID NO: 633) CEP290-194 − AUUAUGCCUAUUUAGUG 17 upstream (SEQ ID NO: 703) CEP290-195 + AUUCCAAGGAACAAAAGCCA 20 upstream (SEQ ID NO: 1118) CEP290-196 − AUUGAGGUAGAAUCAAGAAG 20 downstream (SEQ ID NO: 1119) CEP290-197 + AUUUGACACCACAUGCACUG 20 downstream (SEQ ID NO: 623) CEP290-198 + CAAAAGCCAGGGACCAU 17 upstream (SEQ ID NO: 1120) CEP290-199 − CAACAGUAGCUGAAAUAUUA 20 upstream (SEQ ID NO: 1121) CEP290-200 + CAAGAUGUCUCUUGCCU 17 upstream (SEQ ID NO: 702) CEP290-201 − CAGAACAAACUAUUCUCCCA 20 upstream (SEQ ID NO: 1123) CEP290-202 − CAGAUUUCAUGUGUGAAGAA 20 downstream (SEQ ID NO: 1124) CEP290-204 − CAGCAUUAGAAAGUCCU 17 upstream (SEQ ID NO: 710) CEP290-205 + CAGGGGUAAGAGAAAGGGAU 20 upstream (SEQ ID NO: 1126) CEP290-206 + CAGUAAGGAGGAUGUAAGAC 20 downstream (SEQ ID NO: 676) CEP290-207 − CAGUAGCUGAAAUAUUA 17 upstream (SEQ ID NO: 1128) CEP290-208 + CAUAAGAAAGAACACUG 17 downstream (SEQ ID NO: 665) CEP290-209 + CAUGGGAGAAUAGUUUGUUC 20 upstream (SEQ ID NO: 1130) CEP290-210 + CAUGGGAGUCACAGGGU 17 downstream (SEQ ID NO: 652) CEP290-211 + CAUUCCAAGGAACAAAAGCC 20 upstream (SEQ ID NO: 1131) CEP290-212 + CCACAAGAUGUCUCUUGCCU 20 upstream (SEQ ID NO: 630) CEP290-213 − CCUAGGCAAGAGACAUCUUG 20 upstream (SEQ ID NO: 631) CEP290-214 − CGUGCUCUUUUCUAUAUAUA 20 downstream (SEQ ID NO: 624) CEP290-215 − CGUUGUUCUGAGUAGCUUUC 20 upstream (SEQ ID NO: 629) CEP290-216 + CUAAGACACUGCCAAUA 17 downstream (SEQ ID NO: 597) CEP290-217 + CUAAUGCUGGAGAGGAU 17 upstream (SEQ ID NO: 707) CEP290-218 + CUAGAUGACAUGAGGUAAGU 20 downstream (SEQ ID NO: 671) CEP290-219 + CUAGGACUUUCUAAUGC 17 upstream (SEQ ID NO: 695) CEP290-220 − CUCAUACCUAUCCCUAU 17 downstream (SEQ ID NO: 594) CEP290-221 − CUCCAGCAUUAGAAAGUCCU 20 upstream (SEQ ID NO: 720) CEP290-222 − CUCUAUACCUUUUACUG 17 upstream (SEQ ID NO: 701) CEP290-223 + CUCUUGCUCUAGAUGACAUG 20 downstream (SEQ ID NO: 675) CEP290-224 − CUGCUGCUUUUGCCAAAGAG 20 upstream (SEQ ID NO: 725) CEP290-225 − CUGCUUUUGCCAAAGAG 17 upstream (SEQ ID NO: 711) CEP290-226 − CUGGCUUUUGUUCCUUGGAA 20 upstream (SEQ ID NO: 1140) CEP290-227 + CUGUAAGAUAACUACAA 17 upstream (SEQ ID NO: 1141) CEP290-228 − CUUAAGCAUACUUUUUUUAA 20 downstream (SEQ ID NO: 690) CEP290-229 + CUUAAUAUUUCAGCUACUGU 20 upstream (SEQ ID NO: 1143) CEP290-231 + CUUAGAUGUCUGGUUAAAAG 20 upstream (SEQ ID NO: 1144) CEP290-232 − CUUAUCUAAGAUCCUUUCAC 20 upstream (SEQ ID NO: 734) CEP290-233 + CUUGACUUUUACCCUUC 17 downstream (SEQ ID NO: 649) CEP290-234 + CUUGUUCUGUCCUCAGUAAA 20 upstream (SEQ ID NO: 728) CEP290-235 + CUUUUGACAGUUUUUAAGGC 20 downstream (SEQ ID NO: 684)

Table 8C provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the third tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 8C Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-236 − GAAAUACAAAAACUGGA 17 downstream (SEQ ID NO: 1148) CEP290-237 + GCUUUUGACAGUUUUUA 17 downstream (SEQ ID NO: 634) CEP290-238 + GGAGAUAGAGACAGGAAUAA 20 downstream (SEQ ID NO: 635) CEP290-239 − GGAGUGCAGUGGAGUGAUCU 20 downstream (SEQ ID NO: 1149) CEP290-240 + GGGGUAAGAGAAAGGGA 17 upstream (SEQ ID NO: 1150) CEP290-241 + GGGUAAGAGAAAGGGAU 17 upstream (SEQ ID NO: 1151) CEP290-242 − GUCUCACUGUGUUGCCC 17 downstream (SEQ ID NO: 1152) CEP290-243 − GUGCAGUGGAGUGAUCU 17 downstream (SEQ ID NO: 1153) CEP290-244 + GUGUGUGUGUGUGUGUUAUG 20 upstream (SEQ ID NO: 1154) CEP290-245 + GUGUGUGUGUGUUAUGU 17 upstream (SEQ ID NO: 1155)

Table 8D provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the fourth tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. pyogenes Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 8D Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-246 − AAAUACAAAAACUGGAU 17 downstream (SEQ ID NO: 1156) CEP290-247 − AAGCAUACUUUUUUUAA 17 downstream (SEQ ID NO: 667) CEP290-248 + AAGGCGGGGAGUCACAU 17 downstream (SEQ ID NO: 636) CEP290-249 + AAGUAUGCUUAAGAAAAAAA 20 downstream (SEQ ID NO: 693) CEP290-250 + ACAGAGGACAUGGAGAA 17 upstream (SEQ ID NO: 715) CEP290-251 + ACAGGGGUAAGAGAAAGGGA 20 upstream (SEQ ID NO: 1160) CEP290-253 + ACUAAGACACUGCCAAU 17 downstream (SEQ ID NO: 603) CEP290-254 + ACUCCACUGCACUCCAGCCU 20 downstream (SEQ ID NO: 1161) CEP290-255 + AGACUGGAGAUAGAGAC 17 downstream (SEQ ID NO: 664) CEP290-256 − AGAGUCUCACUGUGUUGCCC 20 downstream (SEQ ID NO: 1163) CEP290-257 + AGAUGAAAAAUACUCUU 17 upstream (SEQ ID NO: 718) CEP290-258 − AUAUUAUCUAUUUAUAG 17 upstream (SEQ ID NO: 1165) CEP290-259 − AUUUCAUGUGUGAAGAA 17 downstream (SEQ ID NO: 1166) CEP290-260 − AUUUUUUAUUAUCUUUAUUG 20 downstream (SEQ ID NO: 694) CEP290-261 + CAACUGGAAGAGAGAAA 17 downstream (SEQ ID NO: 668) CEP290-262 + CACUCCACUGCACUCCAGCC 20 downstream (SEQ ID NO: 1169) CEP290-263 − CACUGUGUUGCCCAGGC 17 downstream (SEQ ID NO: 1170) CEP290-264 + CCAAGGAACAAAAGCCA 17 upstream (SEQ ID NO: 1171) CEP290-265 + CCACUGCACUCCAGCCU 17 downstream (SEQ ID NO: 1172) CEP290-266 − CCCAGGCUGGAGUGCAG 17 downstream (SEQ ID NO: 1173) CEP290-267 − CCCUGGCUUUUGUUCCU 17 upstream (SEQ ID NO: 1174) CEP290-268 + CGCUUGAACCUGGGAGGCAG 20 downstream (SEQ ID NO: 1175) CEP290-269 − UAAGGAAAUACAAAAAC 17 downstream (SEQ ID NO: 1176) CEP290-270 − UAAUAAGGAAAUACAAAAAC 20 downstream (SEQ ID NO: 1177) CEP290-271 − UACUGCAACCUCUGCCUCCC 20 downstream (SEQ ID NO: 1178) CEP290-272 + UAUGCUUAAGAAAAAAA 17 downstream (SEQ ID NO: 669) CEP290-273 + UCAUUCUUGUGGCAGUAAGG 20 downstream (SEQ ID NO: 692) CEP290-274 + UCCACUGCACUCCAGCC 17 downstream (SEQ ID NO: 1181) CEP290-275 − UCUCACUGUGUUGCCCAGGC 20 downstream (SEQ ID NO: 1182) CEP290-276 + UGAACAAGUUUUGAAAC 17 downstream (SEQ ID NO: 659) CEP290-277 − UGCAACCUCUGCCUCCC 17 downstream (SEQ ID NO: 1184) CEP290-278 + UGUGUGUGUGUGUGUUAUGU 20 upstream (SEQ ID NO: 1185) CEP290-279 + UGUGUGUGUGUGUUAUG 17 upstream (SEQ ID NO: 1186) CEP290-280 + UUCUUGUGGCAGUAAGG 17 downstream (SEQ ID NO: 666) CEP290-281 + UUGAACCUGGGAGGCAG 17 downstream (SEQ ID NO: 1188) CEP290-282 − UUGCCCAGGCUGGAGUGCAG 20 downstream (SEQ ID NO: 1189) CEP290-283 − UUUUAUUAUCUUUAUUG 17 downstream (SEQ ID NO: 670)

Table 9A provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, have good orthogonality, start with G and PAM is NNGRRT. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 9A  1st Tier Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-284 + GCUAAAUCAUGCAAGUGACCUAAG 24 upstream (SEQ ID NO: 511) CEP290-487 − GGUCACUUGCAUGAUUUAG 19 upstream (SEQ ID NO: 512) CEP290-486 − GUCACUUGCAUGAUUUAG 18 upstream (SEQ ID NO: 513) CEP290-285 + GCCUAGGACUUUCUAAUGCUGGA 23 upstream (SEQ ID NO: 514) CEP290-479 + GGACUUUCUAAUGCUGGA 18 upstream (SEQ ID NO: 515) CEP290-286 + GGGACCAUGGGAGAAUAGUUUGUU 24 upstream (SEQ ID NO: 516) CEP290-287 + GGACCAUGGGAGAAUAGUUUGUU 23 upstream (SEQ ID NO: 517) CEP290-288 + GACCAUGGGAGAAUAGUUUGUU 22 upstream (SEQ ID NO: 518) CEP290-289 − GGUCCCUGGCUUUUGUUCCUUGGA 24 upstream (SEQ ID NO: 519) CEP290-290 − GUCCCUGGCUUUUGUUCCUUGGA 23 upstream (SEQ ID NO: 520) CEP290-374 − GAAAACGUUGUUCUGAGUAGCUUU 24 upstream (SEQ ID NO: 521) CEP290-478 − GUUGUUCUGAGUAGCUUU 18 upstream (SEQ ID NO: 522) CEP290-489 − GGUCCCUGGCUUUUGUUCCU 20 upstream (SEQ ID NO: 494) CEP290-488 − GUCCCUGGCUUUUGUUCCU 19 upstream (SEQ ID NO: 523) CEP290-291 − GACAUCUUGUGGAUAAUGUAUCA 23 upstream (SEQ ID NO: 524) CEP290-292 − GUCCUAGGCAAGAGACAUCUU 21 upstream (SEQ ID NO: 525) CEP290-293 + GCCAGCAAAAGCUUUUGAGCUAA 23 upstream (SEQ ID NO: 526) CEP290-481 + GCAAAAGCUUUUGAGCUAA 19 upstream (SEQ ID NO: 527) CEP290-294 + GAUCUUAUUCUACUCCUGUGA 21 upstream (SEQ ID NO: 528) CEP290-295 − GCUUUCAGGAUUCCUACUAAAUU 23 upstream (SEQ ID NO: 529) CEP290-323 + GUUCUGUCCUCAGUAAAAGGUA 22 upstream (SEQ ID NO: 530) CEP290-480 + GAACAACGUUUUCAUUUA 18 upstream (SEQ ID NO: 531) CEP290-296 − GUAGAAUAUCAUAAGUUACAAUCU 24 upstream (SEQ ID NO: 532) CEP290-297 − GAAUAUCAUAAGUUACAAUCU 21 upstream (SEQ ID NO: 533) CEP290-298 + GUGGCUGUAAGAUAACUACA 20 upstream (SEQ ID NO: 534) CEP290-299 + GGCUGUAAGAUAACUACA 18 upstream (SEQ ID NO: 535) CEP290-300 − GUUUAACGUUAUCAUUUUCCCA 22 upstream (SEQ ID NO: 536) CEP290-301 + GUAAGAGAAAGGGAUGGGCACUUA 24 upstream (SEQ ID NO: 537) CEP290-492 + GAGAAAGGGAUGGGCACUUA 20 upstream (SEQ ID NO: 538) CEP290-491 + GAAAGGGAUGGGCACUUA 18 upstream (SEQ ID NO: 539) CEP290-483 − GUAAAUGAAAACGUUGUU 18 upstream (SEQ ID NO: 540) CEP290-302 + GAUAAACAUGACUCAUAAUUUAGU 24 upstream (SEQ ID NO: 541) CEP290-303 + GGAACAAAAGCCAGGGACCAUGG 23 upstream (SEQ ID NO: 542) CEP290-304 + GAACAAAAGCCAGGGACCAUGG 22 upstream (SEQ ID NO: 543) CEP290-305 + GGGAGAAUAGUUUGUUCUGGGUAC 24 upstream (SEQ ID NO: 544) CEP290-306 + GGAGAAUAGUUUGUUCUGGGUAC 23 upstream (SEQ ID NO: 545) CEP290-307 + GAGAAUAGUUUGUUCUGGGUAC 22 upstream (SEQ ID NO: 546) CEP290-490 + GAAUAGUUUGUUCUGGGUAC 20 upstream (SEQ ID NO: 468) CEP290-482 − GAAAUAGAGGCUUAUGGAUU 20 upstream (SEQ ID NO: 547) CEP290-308 + GUUCUGGGUACAGGGGUAAGAGAA 24 upstream (SEQ ID NO: 548) CEP290-494 + GGGUACAGGGGUAAGAGAA 19 upstream (SEQ ID NO: 549) CEP290-493 + GGUACAGGGGUAAGAGAA 18 upstream (SEQ ID NO: 550) CEP290-309 − GUAAAUUCUCAUCAUUUUUUAUUG 24 upstream (SEQ ID NO: 551) CEP290-310 + GGAGAGGAUAGGACAGAGGACAUG 24 upstream (SEQ ID NO: 552) CEP290-311 + GAGAGGAUAGGACAGAGGACAUG 23 upstream (SEQ ID NO: 553) CEP290-313 + GAGGAUAGGACAGAGGACAUG 21 upstream (SEQ ID NO: 554) CEP290-485 + GGAUAGGACAGAGGACAUG 19 upstream (SEQ ID NO: 555) CEP290-484 + GAUAGGACAGAGGACAUG 18 upstream (SEQ ID NO: 556) CEP290-314 − GAAUAAAUGUAGAAUUUUAAUG 22 upstream (SEQ ID NO: 557) CEP290-64 − GUCAAAAGCUACCGGUUACCUG 22 downstream (SEQ ID NO: 558) CEP290-315 + GUUUUUAAGGCGGGGAGUCACAU 23 downstream (SEQ ID NO: 559) CEP290-203 − GUCUUACAUCCUCCUUACUGCCAC 24 downstream (SEQ ID NO: 560) CEP290-316 + GAGUCACAGGGUAGGAUUCAUGUU 24 downstream (SEQ ID NO: 561) CEP290-317 + GUCACAGGGUAGGAUUCAUGUU 22 downstream (SEQ ID NO: 562) CEP290-318 − GGCACAGAGUUCAAGCUAAUACAU 24 downstream (SEQ ID NO: 563) CEP290-319 − GCACAGAGUUCAAGCUAAUACAU 23 downstream (SEQ ID NO: 564) CEP290-505 − GAGUUCAAGCUAAUACAU 18 downstream (SEQ ID NO: 565) CEP290-496 + GAUGCAGAACUAGUGUAGAC 20 downstream (SEQ ID NO: 460) CEP290-320 − GUGUUGAGUAUCUCCUGUUUGGCA 24 downstream (SEQ ID NO: 566) CEP290-321 − GUUGAGUAUCUCCUGUUUGGCA 22 downstream (SEQ ID NO: 567) CEP290-504 − GAGUAUCUCCUGUUUGGCA 19 downstream (SEQ ID NO: 568) CEP290-322 − GAAAAUCAGAUUUCAUGUGUG 21 downstream (SEQ ID NO: 569) CEP290-324 − GCCACAAGAAUGAUCAUUCUAAAC 24 downstream (SEQ ID NO: 570) CEP290-325 + GGCGGGGAGUCACAUGGGAGUCA 23 downstream (SEQ ID NO: 571) CEP290-326 + GCGGGGAGUCACAUGGGAGUCA 22 downstream (SEQ ID NO: 572) CEP290-499 + GGGGAGUCACAUGGGAGUCA 20 downstream (SEQ ID NO: 573) CEP290-498 + GGGAGUCACAUGGGAGUCA 19 downstream (SEQ ID NO: 574) CEP290-497 + GGAGUCACAUGGGAGUCA 18 downstream (SEQ ID NO: 575) CEP290-327 + GCUUUUGACAGUUUUUAAGGCG 22 downstream (SEQ ID NO: 576) CEP290-328 + GAUCAUUCUUGUGGCAGUAAG 21 downstream (SEQ ID NO: 577) CEP290-329 − GAGCAAGAGAUGAACUAG 18 downstream (SEQ ID NO: 578) CEP290-500 + GCCUGAACAAGUUUUGAAAC 20 downstream (SEQ ID NO: 480) CEP290-330 − GUAGAUUGAGGUAGAAUCAAGAA 23 downstream (SEQ ID NO: 579) CEP290-506 − GAUUGAGGUAGAAUCAAGAA 20 downstream (SEQ ID NO: 580) CEP290-331 + GGAUGUAAGACUGGAGAUAGAGAC 24 downstream (SEQ ID NO: 581) CEP290-332 + GAUGUAAGACUGGAGAUAGAGAC 23 downstream (SEQ ID NO: 582) CEP290-503 + GUAAGACUGGAGAUAGAGAC 20 downstream (SEQ ID NO: 497) CEP290-333 + GGGAGUCACAUGGGAGUCACAGGG 24 downstream (SEQ ID NO: 583) CEP290-334 + GGAGUCACAUGGGAGUCACAGGG 23 downstream (SEQ ID NO: 584) CEP290-335 + GAGUCACAUGGGAGUCACAGGG 22 downstream (SEQ ID NO: 585) CEP290-502 + GUCACAUGGGAGUCACAGGG 20 downstream (SEQ ID NO: 586) CEP290-336 − GUUUACAUAUCUGUCUUCCUUAA 23 downstream (SEQ ID NO: 587) CEP290-507 − GAUUUCAUGUGUGAAGAA 18 downstream (SEQ ID NO: 588)

Table 9B provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, and have good orthogonality. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 9B Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-337 + AAAUCAUGCAAGUGACCUAAG 21 upstream (SEQ ID NO: 1191) CEP290-338 + AAUCAUGCAAGUGACCUAAG 20 upstream (SEQ ID NO: 1192) CEP290-339 + AUCAUGCAAGUGACCUAAG 19 upstream (SEQ ID NO: 1193) CEP290-340 - AGGUCACUUGCAUGAUUUAG 20 upstream (SEQ ID NO: 1194) CEP290-341 - AAUAUUAAGGGCUCUUCCUGGACC 24 upstream (SEQ ID NO: 1195) CEP290-342 - AUAUUAAGGGCUCUUCCUGGACC 23 upstream (SEQ ID NO: 1196) CEP290-343 - AUUAAGGGCUCUUCCUGGACC 21 upstream (SEQ ID NO: 1197) CEP290-344 - AAGGGCUCUUCCUGGACC 18 upstream (SEQ ID NO: 1198) CEP290-345 + AGGACUUUCUAAUGCUGGA 19 upstream (SEQ ID NO: 1199) CEP290-346 + ACCAUGGGAGAAUAGUUUGUU 21 upstream (SEQ ID NO: 1200) CEP290-347 + AUGGGAGAAUAGUUUGUU 18 upstream (SEQ ID NO: 1201) CEP290-348 + ACUCCUGUGAAAGGAUCUUAGAU 23 upstream (SEQ ID NO: 1202) CEP290-349 - AAAACGUUGUUCUGAGUAGCUUU 23 upstream (SEQ ID NO: 1203) CEP290-350 - AAACGUUGUUCUGAGUAGCUUU 22 upstream (SEQ ID NO: 1204) CEP290-351 - AACGUUGUUCUGAGUAGCUUU 21 upstream (SEQ ID NO: 1205) CEP290-352 - ACGUUGUUCUGAGUAGCUUU 20 upstream (SEQ ID NO: 749) CEP290-353 - AUUUAUAGUGGCUGAAUGACUU 22 upstream (SEQ ID NO: 1207) CEP290-354 - AUAGUGGCUGAAUGACUU 18 upstream (SEQ ID NO: 1208) CEP290-355 - AUGGUCCCUGGCUUUUGUUCCU 22 upstream (SEQ ID NO: 1209) CEP290-356 - AGACAUCUUGUGGAUAAUGUAUCA 24 upstream (SEQ ID NO: 1210) CEP290-357 - ACAUCUUGUGGAUAAUGUAUCA 22 upstream (SEQ ID NO: 1211) CEP290-358 - AUCUUGUGGAUAAUGUAUCA 20 upstream (SEQ ID NO: 835) CEP290-359 - AAAGUCCUAGGCAAGAGACAUCUU 24 upstream (SEQ ID NO: 1213) CEP290-360 - AAGUCCUAGGCAAGAGACAUCUU 23 upstream (SEQ ID NO: 1214) CEP290-361 - AGUCCUAGGCAAGAGACAUCUU 22 upstream (SEQ ID NO: 1215) CEP290-362 + AGCCAGCAAAAGCUUUUGAGCUAA 24 upstream (SEQ ID NO: 1216) CEP290-363 + AGCAAAAGCUUUUGAGCUAA 20 upstream (SEQ ID NO: 763) CEP290-364 + AGAUCUUAUUCUACUCCUGUGA 22 upstream (SEQ ID NO: 1218) CEP290-365 + AUCUUAUUCUACUCCUGUGA 20 upstream (SEQ ID NO: 764) CEP290-366 - AUCUAAGAUCCUUUCACAGGAG 22 upstream (SEQ ID NO: 1220) CEP290-369 - AAGAUCCUUUCACAGGAG 18 upstream (SEQ ID NO: 1221) CEP290-370 - AGCUUUCAGGAUUCCUACUAAAUU 24 upstream (SEQ ID NO: 1222) CEP290-371 + ACUCAGAACAACGUUUUCAUUUA 23 upstream (SEQ ID NO: 1223) CEP290-372 + AGAACAACGUUUUCAUUUA 19 upstream (SEQ ID NO: 1224) CEP290-373 - AGAAUAUCAUAAGUUACAAUCU 22 upstream (SEQ ID NO: 1225) CEP290-375 - AAUAUCAUAAGUUACAAUCU 20 upstream (SEQ ID NO: 1226) CEP290-376 - AUAUCAUAAGUUACAAUCU 19 upstream (SEQ ID NO: 1227) CEP290-377 + AAGUGGCUGUAAGAUAACUACA 22 upstream (SEQ ID NO: 1228) CEP290-378 + AGUGGCUGUAAGAUAACUACA 21 upstream (SEQ ID NO: 1229) CEP290-379 - AUGUUUAACGUUAUCAUUUUCCCA 24 upstream (SEQ ID NO: 1230) CEP290-380 - AACGUUAUCAUUUUCCCA 18 upstream (SEQ ID NO: 1231) CEP290-381 + AAGAGAAAGGGAUGGGCACUUA 22 upstream (SEQ ID NO: 1232) CEP290-382 + AGAGAAAGGGAUGGGCACUUA 21 upstream (SEQ ID NO: 1233) CEP290-383 + AGAAAGGGAUGGGCACUUA 19 upstream (SEQ ID NO: 1234) CEP290-384 - AUUCAGUAAAUGAAAACGUUGUU 23 upstream (SEQ ID NO: 1235) CEP290-385 - AGUAAAUGAAAACGUUGUU 19 upstream (SEQ ID NO: 1236) CEP290-386 + AUAAACAUGACUCAUAAUUUAGU 23 upstream (SEQ ID NO: 1237) CEP290-387 + AAACAUGACUCAUAAUUUAGU 21 upstream (SEQ ID NO: 1238) CEP290-388 + AACAUGACUCAUAAUUUAGU 20 upstream (SEQ ID NO: 721) CEP290-389 + ACAUGACUCAUAAUUUAGU 19 upstream (SEQ ID NO: 1240) CEP290-390 - AUUCUUAUCUAAGAUCCUUUCAC 23 upstream (SEQ ID NO: 1241) CEP290-391 + AGGAACAAAAGCCAGGGACCAUGG 24 upstream (SEQ ID NO: 1242) CEP290-392 + AACAAAAGCCAGGGACCAUGG 21 upstream (SEQ ID NO: 1243) CEP290-393 + ACAAAAGCCAGGGACCAUGG 20 upstream (SEQ ID NO: 1244) CEP290-394 + AAAAGCCAGGGACCAUGG 18 upstream (SEQ ID NO: 1245) CEP290-395 + AGAAUAGUUUGUUCUGGGUAC 21 upstream (SEQ ID NO: 1246) CEP290-396 + AAUAGUUUGUUCUGGGUAC 19 upstream (SEQ ID NO: 1247) CEP290-397 + AUAGUUUGUUCUGGGUAC 18 upstream (SEQ ID NO: 1248) CEP290-398 - AUCAGAAAUAGAGGCUUAUGGAUU 24 upstream (SEQ ID NO: 1249) CEP290-399 - AGAAAUAGAGGCUUAUGGAUU 21 upstream (SEQ ID NO: 1250) CEP290-400 - AAAUAGAGGCUUAUGGAUU 19 upstream (SEQ ID NO: 1251) CEP290-401 - AAUAGAGGCUUAUGGAUU 18 upstream (SEQ ID NO: 1252) CEP290-402 - AAUAUAUUAUCUAUUUAUAGUGG 23 upstream (SEQ ID NO: 1253) CEP290-403 - AUAUAUUAUCUAUUUAUAGUGG 22 upstream (SEQ ID NO: 1254) CEP290-404 - AUAUUAUCUAUUUAUAGUGG 20 upstream (SEQ ID NO: 1255) CEP290-405 - AUUAUCUAUUUAUAGUGG 18 upstream (SEQ ID NO: 1256) CEP290-406 - AAAUUCUCAUCAUUUUUUAUUG 22 upstream (SEQ ID NO: 1257) CEP290-407 - AAUUCUCAUCAUUUUUUAUUG 21 upstream (SEQ ID NO: 1258) CEP290-408 - AUUCUCAUCAUUUUUUAUUG 20 upstream (SEQ ID NO: 1259) CEP290-409 + AGAGGAUAGGACAGAGGACAUG 22 upstream (SEQ ID NO: 1260) CEP290-410 + AGGAUAGGACAGAGGACAUG 20 upstream (SEQ ID NO: 827) CEP290-411 - AGAAUAAAUGUAGAAUUUUAAUG 23 upstream (SEQ ID NO: 1262) CEP290-412 - AAUAAAUGUAGAAUUUUAAUG 21 upstream (SEQ ID NO: 1263) CEP290-413 - AUAAAUGUAGAAUUUUAAUG 20 upstream (SEQ ID NO: 1264) CEP290-414 - AAAUGUAGAAUUUUAAUG 18 upstream (SEQ ID NO: 1265) CEP290-415 - AUUUUUUAUUGUAGAAUAAAUG 22 upstream (SEQ ID NO: 1266) CEP290-416 + CUAAAUCAUGCAAGUGACCUAAG 23 upstream (SEQ ID NO: 1267) CEP290-417 - CCUUAGGUCACUUGCAUGAUUUAG 24 upstream (SEQ ID NO: 1268) CEP290-418 - CUUAGGUCACUUGCAUGAUUUAG 23 upstream (SEQ ID NO: 1269) CEP290-419 + CCUAGGACUUUCUAAUGCUGGA 22 upstream (SEQ ID NO: 1270) CEP290-420 + CUAGGACUUUCUAAUGCUGGA 21 upstream (SEQ ID NO: 1271) CEP290-421 + CCAUGGGAGAAUAGUUUGUU 20 upstream (SEQ ID NO: 1272) CEP290-422 + CAUGGGAGAAUAGUUUGUU 19 upstream (SEQ ID NO: 1273) CEP290-423 + CUCCUGUGAAAGGAUCUUAGAU 22 upstream (SEQ ID NO: 1274) CEP290-424 + CCUGUGAAAGGAUCUUAGAU 20 upstream (SEQ ID NO: 860) CEP290-426 + CUGUGAAAGGAUCUUAGAU 19 upstream (SEQ ID NO: 1276) CEP290-427 - CCCUGGCUUUUGUUCCUUGGA 21 upstream (SEQ ID NO: 1277) CEP290-428 - CCUGGCUUUUGUUCCUUGGA 20 upstream (SEQ ID NO: 1278) CEP290-429 - CUGGCUUUUGUUCCUUGGA 19 upstream (SEQ ID NO: 1279) CEP290-430 - CGUUGUUCUGAGUAGCUUU 19 upstream (SEQ ID NO: 1280) CEP290-431 - CUAUUUAUAGUGGCUGAAUGACUU 24 upstream (SEQ ID NO: 1281) CEP290-432 - CCAUGGUCCCUGGCUUUUGUUCCU 24 upstream (SEQ ID NO: 1282) CEP290-433 - CAUGGUCCCUGGCUUUUGUUCCU 23 upstream (SEQ ID NO: 1283) CEP290-434 - CAUCUUGUGGAUAAUGUAUCA 21 upstream (SEQ ID NO: 1284) CEP290-435 - CUUGUGGAUAAUGUAUCA 18 upstream (SEQ ID NO: 1285) CEP290-437 - CCUAGGCAAGAGACAUCUU 19 upstream (SEQ ID NO: 1286) CEP290-438 - CUAGGCAAGAGACAUCUU 18 upstream (SEQ ID NO: 1287) CEP290-439 + CCAGCAAAAGCUUUUGAGCUAA 22 upstream (SEQ ID NO: 1288) CEP290-440 + CAGCAAAAGCUUUUGAGCUAA 21 upstream (SEQ ID NO: 1289) CEP290-441 + CAAAAGCUUUUGAGCUAA 18 upstream (SEQ ID NO: 1290) CEP290-442 + CUUAUUCUACUCCUGUGA 18 upstream (SEQ ID NO: 1291) CEP290-443 - CUAAGAUCCUUUCACAGGAG 20 upstream (SEQ ID NO: 861) CEP290-444 - CUUCCUCAUCAGAAAUAGAGGCUU 24 upstream (SEQ ID NO: 1293) CEP290-445 - CCUCAUCAGAAAUAGAGGCUU 21 upstream (SEQ ID NO: 1294) CEP290-446 - CUCAUCAGAAAUAGAGGCUU 20 upstream (SEQ ID NO: 865) CEP290-447 - CAUCAGAAAUAGAGGCUU 18 upstream (SEQ ID NO: 1296) CEP290-448 - CUUUCAGGAUUCCUACUAAAUU 22 upstream (SEQ ID NO: 1297) CEP290-449 - CAGGAUUCCUACUAAAUU 18 upstream (SEQ ID NO: 1298) CEP290-450 + CUGUCCUCAGUAAAAGGUA 19 upstream (SEQ ID NO: 1299) CEP290-451 + CUCAGAACAACGUUUUCAUUUA 22 upstream (SEQ ID NO: 1300) CEP290-452 + CAGAACAACGUUUUCAUUUA 20 upstream (SEQ ID NO: 761) CEP290-453 + CAAGUGGCUGUAAGAUAACUACA 23 upstream (SEQ ID NO: 1302) CEP290-454 - CAUUCAGUAAAUGAAAACGUUGUU 24 upstream (SEQ ID NO: 1303) CEP290-457 - CAGUAAAUGAAAACGUUGUU 20 upstream (SEQ ID NO: 849) CEP290-458 + CAUGACUCAUAAUUUAGU 18 upstream (SEQ ID NO: 1305) CEP290-459 - CUUAUCUAAGAUCCUUUCAC 20 upstream (SEQ ID NO: 734) CEP290-460 + CAAAAGCCAGGGACCAUGG 19 upstream (SEQ ID NO: 1307) CEP290-461 - CAGAAAUAGAGGCUUAUGGAUU 22 upstream (SEQ ID NO: 1308) CEP290-462 + CUGGGUACAGGGGUAAGAGAA 21 upstream (SEQ ID NO: 1309) CEP290-463 - CAAUAUAUUAUCUAUUUAUAGUGG 24 upstream (SEQ ID NO: 1310) CEP290-464 - CAUUUUUUAUUGUAGAAUAAAUG 23 upstream (SEQ ID NO: 1311) CEP290-465 + UAAAUCAUGCAAGUGACCUAAG 22 upstream (SEQ ID NO: 1312) CEP290-466 + UCAUGCAAGUGACCUAAG 18 upstream (SEQ ID NO: 1313) CEP290-467 - UUAGGUCACUUGCAUGAUUUAG 22 upstream (SEQ ID NO: 1314) CEP290-468 - UAGGUCACUUGCAUGAUUUAG 21 upstream (SEQ ID NO: 1315) CEP290-469 - UAUUAAGGGCUCUUCCUGGACC 22 upstream (SEQ ID NO: 1316) CEP290-470 - UUAAGGGCUCUUCCUGGACC 20 upstream (SEQ ID NO: 1317) CEP290-471 - UAAGGGCUCUUCCUGGACC 19 upstream (SEQ ID NO: 1318) CEP290-472 + UGCCUAGGACUUUCUAAUGCUGGA 24 upstream (SEQ ID NO: 1319) CEP290-473 + UAGGACUUUCUAAUGCUGGA 20 upstream (SEQ ID NO: 882) CEP290-474 + UACUCCUGUGAAAGGAUCUUAGAU 24 upstream (SEQ ID NO: 1321) CEP290-475 + UCCUGUGAAAGGAUCUUAGAU 21 upstream (SEQ ID NO: 1322) CEP290-476 + UGUGAAAGGAUCUUAGAU 18 upstream (SEQ ID NO: 1323) CEP290-477 - UCCCUGGCUUUUGUUCCUUGGA 22 upstream (SEQ ID NO: 1324) CEP290-515 - UGGCUUUUGUUCCUUGGA 18 upstream (SEQ ID NO: 1325) CEP290-516 - UAUUUAUAGUGGCUGAAUGACUU 23 upstream (SEQ ID NO: 1326) CEP290-517 - UUUAUAGUGGCUGAAUGACUU 21 upstream (SEQ ID NO: 1327) CEP290-518 - UUAUAGUGGCUGAAUGACUU 20 upstream (SEQ ID NO: 1328) CEP290-519 - UAUAGUGGCUGAAUGACUU 19 upstream (SEQ ID NO: 1329) CEP290-520 - UGGUCCCUGGCUUUUGUUCCU 21 upstream (SEQ ID NO: 1330) CEP290-521 - UCCCUGGCUUUUGUUCCU 18 upstream (SEQ ID NO: 1331) CEP290-522 - UCUUGUGGAUAAUGUAUCA 19 upstream (SEQ ID NO: 1332) CEP290-523 - UCCUAGGCAAGAGACAUCUU 20 upstream (SEQ ID NO: 887) CEP290-524 + UUAGAUCUUAUUCUACUCCUGUGA 24 upstream (SEQ ID NO: 1334) CEP290-525 + UAGAUCUUAUUCUACUCCUGUGA 23 upstream (SEQ ID NO: 1335) CEP290-526 + UCUUAUUCUACUCCUGUGA 19 upstream (SEQ ID NO: 1336) CEP290-527 - UUAUCUAAGAUCCUUUCACAGGAG 24 upstream (SEQ ID NO: 1337) CEP290-528 - UAUCUAAGAUCCUUUCACAGGAG 23 upstream  (SEQ ID NO: 1338) CEP290-529 - UCUAAGAUCCUUUCACAGGAG 21 upstream (SEQ ID NO: 1339) CEP290-530 - UAAGAUCCUUUCACAGGAG 19 upstream (SEQ ID NO: 1340) CEP290-531 - UUCCUCAUCAGAAAUAGAGGCUU 23 upstream (SEQ ID NO: 1341) CEP290-532 - UCCUCAUCAGAAAUAGAGGCUU 22 upstream (SEQ ID NO: 1342) CEP290-533 - UCAUCAGAAAUAGAGGCUU 19 upstream (SEQ ID NO: 1343) CEP290-534 - UUUCAGGAUUCCUACUAAAUU 21 upstream (SEQ ID NO: 1344) CEP290-535 - UUCAGGAUUCCUACUAAAUU 20 upstream (SEQ ID NO: 904) CEP290-536 - UCAGGAUUCCUACUAAAUU 19 upstream (SEQ ID NO: 1346) CEP290-537 + UUGUUCUGUCCUCAGUAAAAGGUA 24 upstream (SEQ ID NO: 1347) CEP290-538 + UGUUCUGUCCUCAGUAAAAGGUA 23 upstream (SEQ ID NO: 1348) CEP290-539 + UUCUGUCCUCAGUAAAAGGUA 21 upstream (SEQ ID NO: 1349) CEP290-540 + UCUGUCCUCAGUAAAAGGUA 20 upstream (SEQ ID NO: 890) CEP290-541 + UGUCCUCAGUAAAAGGUA 18 upstream (SEQ ID NO: 1351) CEP290-542 + UACUCAGAACAACGUUUUCAUUUA 24 upstream (SEQ ID NO: 1352) CEP290-543 + UCAGAACAACGUUUUCAUUUA 21 upstream (SEQ ID NO: 1353) CEP290-544 - UAGAAUAUCAUAAGUUACAAUCU 23 upstream (SEQ ID NO: 1354) CEP290-545 - UAUCAUAAGUUACAAUCU 18 upstream (SEQ ID NO: 1355) CEP290-546 + UCAAGUGGCUGUAAGAUAACUACA 24 upstream (SEQ ID NO: 1356) CEP290-547 + UGGCUGUAAGAUAACUACA 19 upstream (SEQ ID NO: 1357) CEP290-548 - UGUUUAACGUUAUCAUUUUCCCA 23 upstream (SEQ ID NO: 1358) CEP290-549 - UUUAACGUUAUCAUUUUCCCA 21 upstream (SEQ ID NO: 1359) CEP290-550 - UUAACGUUAUCAUUUUCCCA 20 upstream (SEQ ID NO: 900) CEP290-551 - UAACGUUAUCAUUUUCCCA 19 upstream (SEQ ID NO: 1361) CEP290-552 + UAAGAGAAAGGGAUGGGCACUUA 23 upstream (SEQ ID NO: 1362) CEP290-553 - UUCAGUAAAUGAAAACGUUGUU 22 upstream (SEQ ID NO: 1363) CEP290-554 - UCAGUAAAUGAAAACGUUGUU 21 upstream (SEQ ID NO: 1364) CEP290-555 + UAAACAUGACUCAUAAUUUAGU 22 upstream (SEQ ID NO: 1365) CEP290-556 - UAUUCUUAUCUAAGAUCCUUUCAC 24 upstream (SEQ ID NO: 1366) CEP290-557 - UUCUUAUCUAAGAUCCUUUCAC 22 upstream (SEQ ID NO: 1367) CEP290-558 - UCUUAUCUAAGAUCCUUUCAC 21 upstream (SEQ ID NO: 1368) CEP290-559 - UUAUCUAAGAUCCUUUCAC 19 upstream (SEQ ID NO: 1369) CEP290-560 - UAUCUAAGAUCCUUUCAC 18 upstream (SEQ ID NO: 1370) CEP290-561 - UCAGAAAUAGAGGCUUAUGGAUU 23 upstream (SEQ ID NO: 1371) CEP290-562 + UUCUGGGUACAGGGGUAAGAGAA 23 upstream (SEQ ID NO: 1372) CEP290-563 + UCUGGGUACAGGGGUAAGAGAA 22 upstream (SEQ ID NO: 1373) CEP290-564 + UGGGUACAGGGGUAAGAGAA 20 upstream (SEQ ID NO: 1374) CEP290-565 - UAUAUUAUCUAUUUAUAGUGG 21 upstream (SEQ ID NO: 1375) CEP290-566 - UAUUAUCUAUUUAUAGUGG 19 upstream (SEQ ID NO: 1376) CEP290-567 - UAAAUUCUCAUCAUUUUUUAUUG 23 upstream (SEQ ID NO: 1377) CEP290-568 - UUCUCAUCAUUUUUUAUUG 19 upstream (SEQ ID NO: 1378) CEP290-569 - UCUCAUCAUUUUUUAUUG 18 upstream (SEQ ID NO: 1379) CEP290-570 - UAGAAUAAAUGUAGAAUUUUAAUG 24 upstream (SEQ ID NO: 1380) CEP290-571 - UAAAUGUAGAAUUUUAAUG 19 upstream (SEQ ID NO: 1381) CEP290-572 - UCAUUUUUUAUUGUAGAAUAAAUG 24 upstream (SEQ ID NO: 1382) CEP290-573 - UUUUUUAUUGUAGAAUAAAUG 21 upstream (SEQ ID NO: 1383) CEP290-574 - UUUUUAUUGUAGAAUAAAUG 20 upstream (SEQ ID NO: 1384) CEP290-575 - UUUUAUUGUAGAAUAAAUG 19 upstream (SEQ ID NO: 1385) CEP290-576 - UUUAUUGUAGAAUAAAUG 18 upstream (SEQ ID NO: 1386) CEP290-577 - AAAAGCUACCGGUUACCUG 19 downstream (SEQ ID NO: 1387) CEP290-578 - AAAGCUACCGGUUACCUG 18 downstream (SEQ ID NO: 1388) CEP290-579 + AGUUUUUAAGGCGGGGAGUCACAU 24 downstream (SEQ ID NO: 1389) CEP290-580 - ACAUCCUCCUUACUGCCAC 19 downstream (SEQ ID NO: 1390) CEP290-581 + AGUCACAGGGUAGGAUUCAUGUU 23 downstream (SEQ ID NO: 1391) CEP290-582 + ACAGGGUAGGAUUCAUGUU 19 downstream (SEQ ID NO: 1392) CEP290-583 - ACAGAGUUCAAGCUAAUACAU 21 downstream (SEQ ID NO: 1393) CEP290-584 - AGAGUUCAAGCUAAUACAU 19 downstream (SEQ ID NO: 1394) CEP290-585 + AUAAGAUGCAGAACUAGUGUAGAC 24 downstream (SEQ ID NO: 1395) CEP290-586 + AAGAUGCAGAACUAGUGUAGAC 22 downstream (SEQ ID NO: 1396) CEP290-587 + AGAUGCAGAACUAGUGUAGAC 21 downstream (SEQ ID NO: 1397) CEP290-588 + AUGCAGAACUAGUGUAGAC 19 downstream (SEQ ID NO: 1398) CEP290-589 - AGUAUCUCCUGUUUGGCA 18 downstream (SEQ ID NO: 1399) CEP290-590 - ACGAAAAUCAGAUUUCAUGUGUG 23 downstream (SEQ ID NO: 1400) CEP290-591 - AAAAUCAGAUUUCAUGUGUG 20 downstream (SEQ ID NO: 1401) CEP290-592 - AAAUCAGAUUUCAUGUGUG 19 downstream (SEQ ID NO: 1402) CEP290-593 - AAUCAGAUUUCAUGUGUG 18 downstream (SEQ ID NO: 1403) CEP290-594 - ACAAGAAUGAUCAUUCUAAAC 21 downstream (SEQ ID NO: 1404) CEP290-595 - AAGAAUGAUCAUUCUAAAC 19 downstream (SEQ ID NO: 1405) CEP290-596 - AGAAUGAUCAUUCUAAAC 18 downstream (SEQ ID NO: 1406) CEP290-597 + AGGCGGGGAGUCACAUGGGAGUCA 24 downstream (SEQ ID NO: 1407) CEP290-598 + AGCUUUUGACAGUUUUUAAGGCG 23 downstream (SEQ ID NO: 1408) CEP290-599 + AAUGAUCAUUCUUGUGGCAGUAAG 24 downstream (SEQ ID NO: 1409) CEP290-600 + AUGAUCAUUCUUGUGGCAGUAAG 23 downstream (SEQ ID NO: 1410) CEP290-601 + AUCAUUCUUGUGGCAGUAAG 20 downstream (SEQ ID NO: 833) CEP290-602 - AUCUAGAGCAAGAGAUGAACUAG 23 downstream (SEQ ID NO: 1412) CEP290-603 - AGAGCAAGAGAUGAACUAG 19 downstream (SEQ ID NO: 1413) CEP290-604 + AAUGCCUGAACAAGUUUUGAAAC 23 downstream (SEQ ID NO: 1414) CEP290-605 + AUGCCUGAACAAGUUUUGAAAC 22 downstream (SEQ ID NO: 1415) CEP290-606 - AGAUUGAGGUAGAAUCAAGAA 21 downstream (SEQ ID NO: 1416) CEP290-607 - AUUGAGGUAGAAUCAAGAA 19 downstream (SEQ ID NO: 1417) CEP290-608 + AUGUAAGACUGGAGAUAGAGAC 22 downstream (SEQ ID NO: 1418) CEP290-609 + AAGACUGGAGAUAGAGAC 18 downstream (SEQ ID NO: 1419) CEP290-610 + AGUCACAUGGGAGUCACAGGG 21 downstream (SEQ ID NO: 1420) CEP290-611 - ACAUAUCUGUCUUCCUUAA 19 downstream (SEQ ID NO: 1421) CEP290-612 - AAAUCAGAUUUCAUGUGUGAAGAA 24 downstream (SEQ ID NO: 1422) CEP290-613 - AAUCAGAUUUCAUGUGUGAAGAA 23 downstream (SEQ ID NO: 1423) CEP290-614 - AUCAGAUUUCAUGUGUGAAGAA 22 downstream (SEQ ID NO: 1424) CEP290-615 - AGAUUUCAUGUGUGAAGAA 19 downstream (SEQ ID NO: 1425) CEP290-616 + AAAUAAAACUAAGACACUGCCAAU 24 downstream (SEQ ID NO: 1025) CEP290-617 + AAUAAAACUAAGACACUGCCAAU 23 downstream (SEQ ID NO: 1026) CEP290-618 + AUAAAACUAAGACACUGCCAAU 22 downstream  (SEQ ID NO: 1027) CEP290-619 + AAAACUAAGACACUGCCAAU 20 downstream (SEQ ID NO: 610) CEP290-620 + AAACUAAGACACUGCCAAU 19 downstream (SEQ ID NO: 1028) CEP290-621 + AACUAAGACACUGCCAAU 18 downstream (SEQ ID NO: 1029) CEP290-622 - AACUAUUUAAUUUGUUUCUGUGUG 24 downstream (SEQ ID NO: 1431) CEP290-623 - ACUAUUUAAUUUGUUUCUGUGUG 23 downstream (SEQ ID NO: 1432) CEP290-624 - AUUUAAUUUGUUUCUGUGUG 20 downstream (SEQ ID NO: 840) CEP290-625 - CUGUCAAAAGCUACCGGUUACCUG 24 downstream (SEQ ID NO: 1434) CEP290-626 - CAAAAGCUACCGGUUACCUG 20 downstream (SEQ ID NO: 755) CEP290-627 - CUUACAUCCUCCUUACUGCCAC 22 downstream (SEQ ID NO: 1436) CEP290-628 - CAUCCUCCUUACUGCCAC 18 downstream (SEQ ID NO: 1437) CEP290-629 + CACAGGGUAGGAUUCAUGUU 20 downstream (SEQ ID NO: 846) CEP290-630 + CAGGGUAGGAUUCAUGUU 18 downstream (SEQ ID NO: 1439) CEP290-631 - CACAGAGUUCAAGCUAAUACAU 22 downstream (SEQ ID NO: 1440) CEP290-632 - CAGAGUUCAAGCUAAUACAU 20 downstream (SEQ ID NO: 848) CEP290-633 - CACGAAAAUCAGAUUUCAUGUGUG 24 downstream (SEQ ID NO: 1442) CEP290-634 - CGAAAAUCAGAUUUCAUGUGUG 22 downstream (SEQ ID NO: 1443) CEP290-635 - CCACAAGAAUGAUCAUUCUAAAC 23 downstream (SEQ ID NO: 1444) CEP290-636 - CACAAGAAUGAUCAUUCUAAAC 22 downstream (SEQ ID NO: 1445) CEP290-637 - CAAGAAUGAUCAUUCUAAAC 20 downstream (SEQ ID NO: 844) CEP290-638 + CGGGGAGUCACAUGGGAGUCA 21 downstream (SEQ ID NO: 1447) CEP290-639 + CUUUUGACAGUUUUUAAGGCG 21 downstream (SEQ ID NO: 1448) CEP290-640 + CAUUCUUGUGGCAGUAAG 18 downstream (SEQ ID NO: 1449) CEP290-641 - CAUCUAGAGCAAGAGAUGAACUAG 24 downstream (SEQ ID NO: 1450) CEP290-642 - CUAGAGCAAGAGAUGAACUAG 21 downstream (SEQ ID NO: 1451) CEP290-643 + CCUGAACAAGUUUUGAAAC 19 downstream (SEQ ID NO: 1452) CEP290-644 + CUGAACAAGUUUUGAAAC 18 downstream (SEQ ID NO: 1453) CEP290-645 - CUCUCUUCCAGUUGUUUUGCUCA 23 downstream (SEQ ID NO: 1454) CEP290-646 - CUCUUCCAGUUGUUUUGCUCA 21 downstream (SEQ ID NO: 1455) CEP290-647 - CUUCCAGUUGUUUUGCUCA 19 downstream (SEQ ID NO: 1456) CEP290-648 + CACAUGGGAGUCACAGGG 18 downstream (SEQ ID NO: 1457) CEP290-649 - CAUAUCUGUCUUCCUUAA 18 downstream (SEQ ID NO: 1458) CEP290-650 - CAGAUUUCAUGUGUGAAGAA 20 downstream (SEQ ID NO: 1124) CEP290-651 - CUAUUUAAUUUGUUUCUGUGUG 22 downstream (SEQ ID NO: 1460) CEP290-652 - UGUCAAAAGCUACCGGUUACCUG 23 downstream (SEQ ID NO: 1461) CEP290-653 - UCAAAAGCUACCGGUUACCUG 21 downstream  (SEQ ID NO: 1462) CEP290-654 + UUUUUAAGGCGGGGAGUCACAU 22 downstream  (SEQ ID NO: 1463) CEP290-655 + UUUUAAGGCGGGGAGUCACAU 21 downstream (SEQ ID NO: 1464) CEP290-656 + UUUAAGGCGGGGAGUCACAU 20 downstream (SEQ ID NO: 619) CEP290-657 + UUAAGGCGGGGAGUCACAU 19 downstream (SEQ ID NO: 1466) CEP290-658 + UAAGGCGGGGAGUCACAU 18 downstream (SEQ ID NO: 1467) CEP290-639 - UCUUACAUCCUCCUUACUGCCAC 23 downstream (SEQ ID NO: 1468) CEP290-660 - UUACAUCCUCCUUACUGCCAC 21 downstream (SEQ ID NO: 1469) CEP290-661 - UACAUCCUCCUUACUGCCAC 20 downstream (SEQ ID NO: 875) CEP290-662 + UCACAGGGUAGGAUUCAUGUU 21 downstream (SEQ ID NO: 1471) CEP290-663 + UAAGAUGCAGAACUAGUGUAGAC 23 downstream (SEQ ID NO: 1472) CEP290-664 + UGCAGAACUAGUGUAGAC 18 downstream (SEQ ID NO: 1473) CEP290-665 - UGUUGAGUAUCUCCUGUUUGGCA 23 downstream (SEQ ID NO: 1474) CEP290-666 - UUGAGUAUCUCCUGUUUGGCA 21 downstream (SEQ ID NO: 1475) CEP290-667 - UGAGUAUCUCCUGUUUGGCA 20 downstream (SEQ ID NO: 895) CEP290-668 + UAGCUUUUGACAGUUUUUAAGGCG 24 downstream (SEQ ID NO: 1477) CEP290-669 + UUUUGACAGUUUUUAAGGCG 20 downstream (SEQ ID NO: 681) CEP290-670 + UUUGACAGUUUUUAAGGCG 19 downstream (SEQ ID NO: 1479) CEP290-671 + UUGACAGUUUUUAAGGCG 18 downstream (SEQ ID NO: 1480) CEP290-672 + UGAUCAUUCUUGUGGCAGUAAG 22 downstream (SEQ ID NO: 1481) CEP290-673 + UCAUUCUUGUGGCAGUAAG 19 downstream (SEQ ID NO: 1482) CEP290-674 - UCUAGAGCAAGAGAUGAACUAG 22 downstream (SEQ ID NO: 1483) CEP290-675 - UAGAGCAAGAGAUGAACUAG 20 downstream (SEQ ID NO: 878) CEP290-676 + UAAUGCCUGAACAAGUUUUGAAAC 24 downstream (SEQ ID NO: 1485) CEP290-677 + UGCCUGAACAAGUUUUGAAAC 21 downstream (SEQ ID NO: 1486) CEP290-678 - UGUAGAUUGAGGUAGAAUCAAGAA 24 downstream (SEQ ID NO: 1487) CEP290-679 - UAGAUUGAGGUAGAAUCAAGAA 22 downstream (SEQ ID NO: 1488) CEP290-680 - UUGAGGUAGAAUCAAGAA 18 downstream (SEQ ID NO: 1489) CEP290-681 + UGUAAGACUGGAGAUAGAGAC 21 downstream (SEQ ID NO: 1490) CEP290-682 + UAAGACUGGAGAUAGAGAC 19 downstream (SEQ ID NO: 1491) CEP290-683 - UCUCUCUUCCAGUUGUUUUGCUCA 24 downstream (SEQ ID NO: 1492) CEP290-684 - UCUCUUCCAGUUGUUUUGCUCA 22 downstream (SEQ ID NO: 1493) CEP290-685 - UCUUCCAGUUGUUUUGCUCA 20 downstream (SEQ ID NO: 893) CEP290-686 - UUCCAGUUGUUUUGCUCA 18 downstream (SEQ ID NO: 1495) CEP290-687 + UCACAUGGGAGUCACAGGG 19 downstream (SEQ ID NO: 1496) CEP290-688 - UGUUUACAUAUCUGUCUUCCUUAA 24 downstream (SEQ ID NO: 1497) CEP290-689 - UUUACAUAUCUGUCUUCCUUAA 22 downstream (SEQ ID NO: 1498) CEP290-690 - UUACAUAUCUGUCUUCCUUAA 21 downstream (SEQ ID NO: 1499) CEP290-691 - UACAUAUCUGUCUUCCUUAA 20 downstream (SEQ ID NO: 689) CEP290-692 - UCAGAUUUCAUGUGUGAAGAA 21 downstream (SEQ ID NO: 1501) CEP290-693 + UAAAACUAAGACACUGCCAAU 21 downstream (SEQ ID NO: 1035) CEP290-694 - UAUUUAAUUUGUUUCUGUGUG 21 downstream (SEQ ID NO: 1503) CEP290-695 - UUUAAUUUGUUUCUGUGUG 19 downstream (SEQ ID NO: 1504) CEP290-696 - UUAAUUUGUUUCUGUGUG 18 downstream (SEQ ID NO: 1505)

Table 9C provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the third tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, start with G and PAM is NNGRRT. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 9C Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-697 - GUAGAAUAAAUUUAUUUAAUG 21 upstream (SEQ ID NO: 1506) CEP290-495 - GAAUAAAUUUAUUUAAUG 18 upstream (SEQ ID NO: 1507) CEP290-698 - GAGAAAAAGGAGCAUGAAACAGG 23 upstream (SEQ ID NO: 1508) CEP290-699 - GAAAAAGGAGCAUGAAACAGG 21 upstream (SEQ ID NO: 1509) CEP290-700 - GUAGAAUAAAAAAUAAAAAAAC 22 upstream (SEQ ID NO: 1510) CEP290-701 - GAAUAAAAAAUAAAAAAAC 19 upstream (SEQ ID NO: 1511) CEP290-702 - GAAUAAAAAAUAAAAAAACUAGAG 24 upstream (SEQ ID NO: 1512) CEP290-508 - GAAAUAGAUGUAGAUUGAGG 20 downstream (SEQ ID NO: 1513) CEP290-703 - GAUAAUAAGGAAAUACAAAAA 21 downstream (SEQ ID NO: 1514) CEP290-704 - GUGUUGCCCAGGCUGGAGUGCAG 23 downstream (SEQ ID NO: 1515) CEP290-705 - GUUGCCCAGGCUGGAGUGCAG 21 downstream (SEQ ID NO: 1516) CEP290-706 - GCCCAGGCUGGAGUGCAG 18 downstream (SEQ ID NO: 1517) CEP290-707 - GUUGUUUUUUUUUUUGAAA 19 downstream (SEQ ID NO: 1518) CEP290-708 - GAGUCUCACUGUGUUGCCCAGGC 23 downstream (SEQ ID NO: 1519) CEP290-709 - GUCUCACUGUGUUGCCCAGGC 21 downstream (SEQ ID NO: 1520)

Table 9D provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the fourth tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation and PAM is NNGRRT. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 9D Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-710 - AAUGUAGAAUAAAUUUAUUUAAUG 24 upstream (SEQ ID NO: 1521) CEP290-711 - AUGUAGAAUAAAUUUAUUUAAUG 23 upstream (SEQ ID NO: 1522) CEP290-712 - AGAAUAAAUUUAUUUAAUG 19 upstream (SEQ ID NO: 1523) CEP290-713 + AUUUAUUCUACAAUAAAAAAUGAU 24 upstream (SEQ ID NO: 1524) CEP290-714 + AUUCUACAAUAAAAAAUGAU 20 upstream (SEQ ID NO: 1525) CEP290-715 - AGAGAAAAAGGAGCAUGAAACAGG 24 upstream (SEQ ID NO: 1526) CEP290-716 - AGAAAAAGGAGCAUGAAACAGG 22 upstream (SEQ ID NO: 1527) CEP290-717 - AAAAAGGAGCAUGAAACAGG 20 upstream (SEQ ID NO: 1528) CEP290-718 - AAAAGGAGCAUGAAACAGG 19 upstream (SEQ ID NO: 1529) CEP290-719 - AAAGGAGCAUGAAACAGG 18 upstream (SEQ ID NO: 1530) CEP290-720 + ACAAUAAAAAAUGAUGAGAAUUUA 24 upstream (SEQ ID NO: 1531) CEP290-721 + AAUAAAAAAUGAUGAGAAUUUA 22 upstream (SEQ ID NO: 1532) CEP290-722 + AUAAAAAAUGAUGAGAAUUUA 21 upstream (SEQ ID NO: 1533) CEP290-723 + AAAAAAUGAUGAGAAUUUA 19 upstream (SEQ ID NO: 1534) CEP290-724 + AAAAAUGAUGAGAAUUUA 18 upstream (SEQ ID NO: 1535) CEP290-725 - AUGUAGAAUAAAAAAUAAAAAAAC 24 upstream (SEQ ID NO: 1536) CEP290-726 - AGAAUAAAAAAUAAAAAAAC 20 upstream (SEQ ID NO: 1537) CEP290-727 - AAUAAAAAAUAAAAAAAC 18 upstream (SEQ ID NO: 1538) CEP290-728 - AAUAAAAAAUAAAAAAACUAGAG 23 upstream (SEQ ID NO: 1539) CEP290-729 - AUAAAAAAUAAAAAAACUAGAG 22 upstream (SEQ ID NO: 1540) CEP290-730 - AAAAAAUAAAAAAACUAGAG 20 upstream (SEQ ID NO: 1541) CEP290-731 - AAAAAUAAAAAAACUAGAG 19 upstream (SEQ ID NO: 1542) CEP290-732 - AAAAUAAAAAAACUAGAG 18 upstream (SEQ ID NO: 1543) CEP290-733 + CAAUAAAAAAUGAUGAGAAUUUA 23 upstream (SEQ ID NO: 1544) CEP290-734 - UGUAGAAUAAAUUUAUUUAAUG 22 upstream (SEQ ID NO: 1545) CEP290-735 - UAGAAUAAAUUUAUUUAAUG 20 upstream (SEQ ID NO: 1546) CEP290-736 + UUUAUUCUACAAUAAAAAAUGAU 23 upstream (SEQ ID NO: 1547) CEP290-737 + UUAUUCUACAAUAAAAAAUGAU 22 upstream (SEQ ID NO: 1548) CEP290-738 + UAUUCUACAAUAAAAAAUGAU 21 upstream (SEQ ID NO: 1549) CEP290-739 + UUCUACAAUAAAAAAUGAU 19 upstream (SEQ ID NO: 1550) CEP290-740 + UCUACAAUAAAAAAUGAU 18 upstream (SEQ ID NO: 1551) CEP290-741 + UAAAAAAUGAUGAGAAUUUA 20 upstream (SEQ ID NO: 1552) CEP290-742 - UGUAGAAUAAAAAAUAAAAAAAC 23 upstream (SEQ ID NO: 1553) CEP290-743 - UAGAAUAAAAAAUAAAAAAAC 21 upstream (SEQ ID NO: 1554) CEP290-744 - UAAAAAAUAAAAAAACUAGAG 21 upstream (SEQ ID NO: 1555) CEP290-745 - AAAAGAAAUAGAUGUAGAUUGAGG 24 downstream (SEQ ID NO: 1556) CEP290-746 - AAAGAAAUAGAUGUAGAUUGAGG 23 downstream (SEQ ID NO: 1557) CEP290-747 - AAGAAAUAGAUGUAGAUUGAGG 22 downstream (SEQ ID NO: 1558) CEP290-748 - AGAAAUAGAUGUAGAUUGAGG 21 downstream (SEQ ID NO: 1559) CEP290-749 - AAAUAGAUGUAGAUUGAGG 19 downstream (SEQ ID NO: 1560) CEP290-750 - AAUAGAUGUAGAUUGAGG 18 downstream (SEQ ID NO: 1561) CEP290-751 - AUAAUAAGGAAAUACAAAAACUGG 24 downstream (SEQ ID NO: 1562) CEP290-752 - AAUAAGGAAAUACAAAAACUGG 22 downstream (SEQ ID NO: 1563) CEP290-753 - AUAAGGAAAUACAAAAACUGG 21 downstream (SEQ ID NO: 1564) CEP290-754 - AAGGAAAUACAAAAACUGG 19 downstream (SEQ ID NO: 1565) CEP290-755 - AGGAAAUACAAAAACUGG 18 downstream (SEQ ID NO: 1566) CEP290-756 - AUAGAUAAUAAGGAAAUACAAAAA 24 downstream (SEQ ID NO: 1567) CEP290-757 - AGAUAAUAAGGAAAUACAAAAA 22 downstream (SEQ ID NO: 1568) CEP290-758 - AUAAUAAGGAAAUACAAAAA 20 downstream (SEQ ID NO: 1569) CEP290-759 - AAUAAGGAAAUACAAAAA 18 downstream (SEQ ID NO: 1570) CEP290-760 + AAAAAAAAAAACAACAAAAA 20 downstream (SEQ ID NO: 1571) CEP290-761 + AAAAAAAAAACAACAAAAA 19 downstream (SEQ ID NO: 1572) CEP290-762 + AAAAAAAAACAACAAAAA 18 downstream (SEQ ID NO: 1573) CEP290-763 - AGAGUCUCACUGUGUUGCCCAGGC 24 downstream (SEQ ID NO: 1574) CEP290-764 - AGUCUCACUGUGUUGCCCAGGC 22 downstream (SEQ ID NO: 1575) CEP290-765 + CAAAAAAAAAAACAACAAAAA 21 downstream (SEQ ID NO: 1576) CEP290-766 - CUCACUGUGUUGCCCAGGC 19 downstream (SEQ ID NO: 1577) CEP290-767 - UAAUAAGGAAAUACAAAAACUGG 23 downstream (SEQ ID NO: 1578) CEP290-768 - UAAGGAAAUACAAAAACUGG 20 downstream (SEQ ID NO: 1579) CEP290-769 - UAGAUAAUAAGGAAAUACAAAAA 23 downstream (SEQ ID NO: 1580) CEP290-770 - UAAUAAGGAAAUACAAAAA 19 downstream (SEQ ID NO: 1581) CEP290-771 - UGUGUUGCCCAGGCUGGAGUGCAG 24 downstream (SEQ ID NO: 1582) CEP290-772 - UGUUGCCCAGGCUGGAGUGCAG 22 downstream (SEQ ID NO: 1583) CEP290-773 - UUGCCCAGGCUGGAGUGCAG 20 downstream (SEQ ID NO: 1189) CEP290-774 - UGCCCAGGCUGGAGUGCAG 19 downstream (SEQ ID NO: 1585) CEP290-775 + UUUCAAAAAAAAAAACAACAAAAA 24 downstream (SEQ ID NO: 1586) CEP290-776 + UUCAAAAAAAAAAACAACAAAAA 23 downstream (SEQ ID NO: 1587) CEP290-777 + UCAAAAAAAAAAACAACAAAAA 22 downstream (SEQ ID NO: 1588) CEP290-778 - UUUUUGUUGUUUUUUUUUUUGAAA 24 downstream (SEQ ID NO: 1589) CEP290-779 - UUUUGUUGUUUUUUUUUUUGAAA 23 downstream (SEQ ID NO: 1590) CEP290-780 - UUUGUUGUUUUUUUUUUUGAAA 22 downstream (SEQ ID NO: 1591) CEP290-781 - UUGUUGUUUUUUUUUUUGAAA 21 downstream (SEQ ID NO: 1592) CEP290-782 - UGUUGUUUUUUUUUUUGAAA 20 downstream (SEQ ID NO: 1593) CEP290-783 - UUGUUUUUUUUUUUGAAA 18 downstream (SEQ ID NO: 1594) CEP290-784 - UCUCACUGUGUUGCCCAGGC 20 downstream (SEQ ID NO: 1182) CEP290-785 - UCACUGUGUUGCCCAGGC 18 downstream (SEQ ID NO: 1596)

Table 9E provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the fifth tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation and PAM is NNGRRV. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a S. aureus Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 9E Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-786 + ACUGUUGGCUACAUCCAUUCC 21 upstream (SEQ ID NO: 1597) CEP290-787 + AAUUUACAGAGUGCAUCCAUGGUC 24 upstream (SEQ ID NO: 1598) CEP290-788 + AUUUACAGAGUGCAUCCAUGGUC 23 upstream (SEQ ID NO: 1599) CEP290-789 + ACAGAGUGCAUCCAUGGUC 19 upstream (SEQ ID NO: 1600) CEP290-790 - AGCAUUAGAAAGUCCUAGGC 20 upstream (SEQ ID NO: 823) CEP290-791 - AUGGUCCCUGGCUUUUGUUCC 21 upstream (SEQ ID NO: 1602) CEP290-792 - AUAGAGACACAUUCAGUAA 19 upstream (SEQ ID NO: 1603) CEP290-793 - AGCUCAAAAGCUUUUGCUGGCUCA 24 upstream (SEQ ID NO: 1604) CEP290-794 - AAAAGCUUUUGCUGGCUCA 19 upstream (SEQ ID NO: 1605) CEP290-795 - AAAGCUUUUGCUGGCUCA 18 upstream (SEQ ID NO: 1606) CEP290-796 + AAUCCAUAAGCCUCUAUUUCUGAU 24 upstream (SEQ ID NO: 1607) CEP290-797 + AUCCAUAAGCCUCUAUUUCUGAU 23 upstream (SEQ ID NO: 1608) CEP290-798 + AUAAGCCUCUAUUUCUGAU 19 upstream (SEQ ID NO: 1609) CEP290-799 + AGCUAAAUCAUGCAAGUGACCUA 23 upstream (SEQ ID NO: 1610) CEP290-800 + AAAUCAUGCAAGUGACCUA 19 upstream (SEQ ID NO: 1611) CEP290-801 + AAUCAUGCAAGUGACCUA 18 upstream (SEQ ID NO: 1612) CEP290-802 - AAACCUCUUUUAACCAGACAUCU 23 upstream (SEQ ID NO: 1613) CEP290-803 - AACCUCUUUUAACCAGACAUCU 22 upstream (SEQ ID NO: 1614) CEP290-804 - ACCUCUUUUAACCAGACAUCU 21 upstream (SEQ ID NO: 1615) CEP290-805 + AGUUUGUUCUGGGUACAGGGGUAA 24 upstream (SEQ ID NO: 1616) CEP290-806 + AUGACUCAUAAUUUAGUAGGAAUC 24 upstream  (SEQ ID NO: 1617) CEP290-807 + ACUCAUAAUUUAGUAGGAAUC 21 upstream (SEQ ID NO: 1618) CEP290-808 - AAUGGAUGUAGCCAACAGUAG 21 upstream (SEQ ID NO: 1619) CEP290-809 - AUGGAUGUAGCCAACAGUAG 20 upstream (SEQ ID NO: 1620) CEP290-810 + AUCACCUCUCUUUGGCAAAAGCAG 24 upstream (SEQ ID NO: 1621) CEP290-811 + ACCUCUCUUUGGCAAAAGCAG 21 upstream (SEQ ID NO: 1622) CEP290-812 - AGGUAGAAUAUUGUAAUCAAAGG 23 upstream (SEQ ID NO: 1623) CEP290-813 - AGAAUAUUGUAAUCAAAGG 19 upstream (SEQ ID NO: 1624) CEP290-814 + AAGGAACAAAAGCCAGGGACC 21 upstream (SEQ ID NO: 1625) CEP290-815 + AGGAACAAAAGCCAGGGACC 20 upstream (SEQ ID NO: 1626) CEP290-816 + ACAUCCAUUCCAAGGAACAAAAGC 24 upstream (SEQ ID NO: 1627) CEP290-817 + AUCCAUUCCAAGGAACAAAAGC 22 upstream (SEQ ID NO: 1628) CEP290-818 + AUUCCAAGGAACAAAAGC 18 upstream (SEQ ID NO: 1629) CEP290-819 + AGAAUUAGAUCUUAUUCUACUCCU 24 upstream (SEQ ID NO: 1630) CEP290-820 + AAUUAGAUCUUAUUCUACUCCU 22 upstream (SEQ ID NO: 1631) CEP290-821 + AUUAGAUCUUAUUCUACUCCU 21 upstream (SEQ ID NO: 1632) CEP290-822 + AGAUCUUAUUCUACUCCU 18 upstream (SEQ ID NO: 1633) CEP290-823 - AUUUGUUCAUCUUCCUCAU 19 upstream (SEQ ID NO: 1634) CEP290-824 - AGAGGUGAUUAUGUUACUUUUUA 23 upstream (SEQ ID NO: 1635) CEP290-825 - AGGUGAUUAUGUUACUUUUUA 21 upstream (SEQ ID NO: 1636) CEP290-826 - AACCUCUUUUAACCAGACAUCUAA 24 upstream (SEQ ID NO: 1637) CEP290-827 - ACCUCUUUUAACCAGACAUCUAA 23 upstream (SEQ ID NO: 1638) CEP290-828 + AUAAACAUGACUCAUAAUUUAG 22 upstream (SEQ ID NO: 1639) CEP290-829 + AAACAUGACUCAUAAUUUAG 20 upstream (SEQ ID NO: 805) CEP290-830 + AACAUGACUCAUAAUUUAG 19 upstream (SEQ ID NO: 1641) CEP290-831 + ACAUGACUCAUAAUUUAG 18 upstream (SEQ ID NO: 1642) CEP290-832 - ACAGGUAGAAUAUUGUAAUCAAAG 24 upstream (SEQ ID NO: 1643) CEP290-833 - AGGUAGAAUAUUGUAAUCAAAG 22 upstream (SEQ ID NO: 1644) CEP290-834 - AGAAUAUUGUAAUCAAAG 18 upstream (SEQ ID NO: 1645) CEP290-835 + AUAGUUUGUUCUGGGUACAGGGGU 24 upstream (SEQ ID NO: 1646) CEP290-836 + AGUUUGUUCUGGGUACAGGGGU 22 upstream (SEQ ID NO: 1647) CEP290-837 - AGACAUCUAAGAGAAAAAGGAGC 23 upstream (SEQ ID NO: 1648) CEP290-838 - ACAUCUAAGAGAAAAAGGAGC 21 upstream (SEQ ID NO: 1649) CEP290-839 - AUCUAAGAGAAAAAGGAGC 19 upstream  (SEQ ID NO: 1650) CEP290-840 + AGAGGAUAGGACAGAGGACA 20 upstream (SEQ ID NO: 735) CEP290-841 + AGGAUAGGACAGAGGACA 18 upstream (SEQ ID NO: 1652) CEP290-842 + AGGAAAGAUGAAAAAUACUCUU 22 upstream (SEQ ID NO: 1653) CEP290-843 + AAAGAUGAAAAAUACUCUU 19 upstream (SEQ ID NO: 1654) CEP290-844 + AAGAUGAAAAAUACUCUU 18 upstream (SEQ ID NO: 1655) CEP290-845 + AGGAAAGAUGAAAAAUACUCUUU 23 upstream (SEQ ID NO: 1656) CEP290-846 + AAAGAUGAAAAAUACUCUUU 20 upstream (SEQ ID NO: 737) CEP290-847 + AAGAUGAAAAAUACUCUUU 19 upstream (SEQ ID NO: 1658) CEP290-848 + AGAUGAAAAAUACUCUUU 18 upstream (SEQ ID NO: 1659) CEP290-849 + AGGAAAGAUGAAAAAUACUCU 21 upstream (SEQ ID NO: 1660) CEP290-850 + AAAGAUGAAAAAUACUCU 18 upstream (SEQ ID NO: 1661) CEP290-851 + AUAGGACAGAGGACAUGGAGAA 22 upstream (SEQ ID NO: 1662) CEP290-852 + AGGACAGAGGACAUGGAGAA 20 upstream (SEQ ID NO: 736) CEP290-853 + AGGAUAGGACAGAGGACAUGGAGA 24 upstream (SEQ ID NO: 1664) CEP290-854 + AUAGGACAGAGGACAUGGAGA 21 upstream (SEQ ID NO: 1665) CEP290-855 + AGGACAGAGGACAUGGAGA 19 upstream (SEQ ID NO: 1666) CEP290-856 + AAGGAACAAAAGCCAGGGACCAU 23 upstream (SEQ ID NO: 1667) CEP290-857 + AGGAACAAAAGCCAGGGACCAU 22 upstream (SEQ ID NO: 1668) CEP290-858 + AACAAAAGCCAGGGACCAU 19 upstream (SEQ ID NO: 1669) CEP290-859 + ACAAAAGCCAGGGACCAU 18 upstream (SEQ ID NO: 1670) CEP290-860 + ACAUUUAUUCUACAAUAAAAAAUG 24 upstream (SEQ ID NO: 1671) CEP290-861 + AUUUAUUCUACAAUAAAAAAUG 22 upstream (SEQ ID NO: 1672) CEP290-862 + AUUCUACAAUAAAAAAUG 18 upstream (SEQ ID NO: 1673) CEP290-863 + AUUGUGUGUGUGUGUGUGUGUUAU 24 upstream (SEQ ID NO: 1674) CEP290-864 + CUACUGUUGGCUACAUCCAUUCC 23 upstream (SEQ ID NO: 1675) CEP290-865 + CUGUUGGCUACAUCCAUUCC 20 upstream (SEQ ID NO: 1676) CEP290-866 + CAGAGUGCAUCCAUGGUC 18 upstream (SEQ ID NO: 1677) CEP290-867 - CUCCAGCAUUAGAAAGUCCUAGGC 24 upstream (SEQ ID NO: 1678) CEP290-868 - CCAGCAUUAGAAAGUCCUAGGC 22 upstream (SEQ ID NO: 1679) CEP290-869 - CAGCAUUAGAAAGUCCUAGGC 21 upstream (SEQ ID NO: 1680) CEP290-870 - CAUUAGAAAGUCCUAGGC 18 upstream (SEQ ID NO: 1681) CEP290-871 - CCCAUGGUCCCUGGCUUUUGUUCC 24 upstream (SEQ ID NO: 1682) CEP290-872 - CCAUGGUCCCUGGCUUUUGUUCC 23 upstream (SEQ ID NO: 1683) CEP290-873 - CAUGGUCCCUGGCUUUUGUUCC 22 upstream (SEQ ID NO: 1684) CEP290-874 - CUCAUAGAGACACAUUCAGUAA 22 upstream (SEQ ID NO: 1685) CEP290-875 - CAUAGAGACACAUUCAGUAA 20 upstream (SEQ ID NO: 750) CEP290-876 - CUCAAAAGCUUUUGCUGGCUCA 22 upstream (SEQ ID NO: 1687) CEP290-877 - CAAAAGCUUUUGCUGGCUCA 20 upstream (SEQ ID NO: 762) CEP290-878 + CCAUAAGCCUCUAUUUCUGAU 21 upstream (SEQ ID NO: 1689) CEP290-879 + CAUAAGCCUCUAUUUCUGAU 20 upstream (SEQ ID NO: 851) CEP290-880 + CAGCUAAAUCAUGCAAGUGACCUA 24 upstream (SEQ ID NO: 1691) CEP290-881 + CUAAAUCAUGCAAGUGACCUA 21 upstream (SEQ ID NO: 1692) CEP290-882 - CAAACCUCUUUUAACCAGACAUCU 24 upstream (SEQ ID NO: 1693) CEP290-883 - CCUCUUUUAACCAGACAUCU 20 upstream (SEQ ID NO: 1694) CEP290-884 - CUCUUUUAACCAGACAUCU 19 upstream  (SEQ ID NO: 1695) CEP290-885 + CUCAUAAUUUAGUAGGAAUC 20 upstream (SEQ ID NO: 864) CEP290-886 + CAUAAUUUAGUAGGAAUC 18 upstream (SEQ ID NO: 1697) CEP290-887 + CACCUCUCUUUGGCAAAAGCAG 22 upstream (SEQ ID NO: 1698) CEP290-888 + CCUCUCUUUGGCAAAAGCAG 20 upstream (SEQ ID NO: 859) CEP290-889 + CUCUCUUUGGCAAAAGCAG 19 upstream (SEQ ID NO: 1700) CEP290-890 - CAGGUAGAAUAUUGUAAUCAAAGG 24 upstream (SEQ ID NO: 1701) CEP290-891 + CCAAGGAACAAAAGCCAGGGACC 23 upstream (SEQ ID NO: 1702) CEP290-892 + CAAGGAACAAAAGCCAGGGACC 22 upstream (SEQ ID NO: 1703) CEP290-893 + CAUCCAUUCCAAGGAACAAAAGC 23 upstream (SEQ ID NO: 1704) CEP290-894 + CCAUUCCAAGGAACAAAAGC 20 upstream (SEQ ID NO: 1705) CEP290-895 + CAUUCCAAGGAACAAAAGC 19 upstream (SEQ ID NO: 1706) CEP290-896 + CUCUUGCCUAGGACUUUCUAAUGC 24 upstream (SEQ ID NO: 1707) CEP290-897 + CUUGCCUAGGACUUUCUAAUGC 22 upstream (SEQ ID NO: 1708) CEP290-898 + CCUAGGACUUUCUAAUGC 18 upstream (SEQ ID NO: 1709) CEP290-899 - CCUGAUUUGUUCAUCUUCCUCAU 23 upstream (SEQ ID NO: 1710) CEP290-900 - CUGAUUUGUUCAUCUUCCUCAU 22 upstream (SEQ ID NO: 1711) CEP290-901 - CCUCUUUUAACCAGACAUCUAA 22 upstream (SEQ ID NO: 1712) CEP290-902 - CUCUUUUAACCAGACAUCUAA 21 upstream (SEQ ID NO: 1713) CEP290-903 - CUUUUAACCAGACAUCUAA 19 upstream (SEQ ID NO: 1714) CEP290-904 - CCUCUGUCCUAUCCUCUCCAGCAU 24 upstream (SEQ ID NO: 1715) CEP290-905 - CUCUGUCCUAUCCUCUCCAGCAU 23 upstream (SEQ ID NO: 1716) CEP290-906 - CUGUCCUAUCCUCUCCAGCAU 21 upstream (SEQ ID NO: 1717) CEP290-907 - CAGGUAGAAUAUUGUAAUCAAAG 23 upstream (SEQ ID NO: 1718) CEP290-908 CUGGGUACAGGGGUAAGAGA 20 upstream (SEQ ID NO: 1719) CEP290-909 - CUUUCUGCUGCUUUUGCCA 19 upstream (SEQ ID NO: 1720) CEP290-910 - CAGACAUCUAAGAGAAAAAGGAGC 24 upstream (SEQ ID NO: 1721) CEP290-911 - CAUCUAAGAGAAAAAGGAGC 20 upstream (SEQ ID NO: 1722) CEP290-912 + CUGGAGAGGAUAGGACAGAGGACA 24 upstream (SEQ ID NO: 1723) CEP290-913 + CAAGGAACAAAAGCCAGGGACCAU 24 upstream (SEQ ID NO: 1724) CEP290-914 + CAUUUAUUCUACAAUAAAAAAUG 23 upstream (SEQ ID NO: 1725) CEP290-915 + GCUACUGUUGGCUACAUCCAUUCC 24 upstream (SEQ ID NO: 1726) CEP290-916 + GUUGGCUACAUCCAUUCC 18 upstream (SEQ ID NO: 1727) CEP290-917 - GCAUUAGAAAGUCCUAGGC 19 upstream (SEQ ID NO: 1728) CEP290-918 - GGUCCCUGGCUUUUGUUCC 19 upstream (SEQ ID NO: 1729) CEP290-919 - GUCCCUGGCUUUUGUUCC 18 upstream (SEQ ID NO: 1730) CEP290-920 - GGCUCAUAGAGACACAUUCAGUAA 24 upstream (SEQ ID NO: 1731) CEP290-921 - GCUCAUAGAGACACAUUCAGUAA 23 upstream (SEQ ID NO: 1732) CEP290-922 - GCUCAAAAGCUUUUGCUGGCUCA 23 upstream  (SEQ ID NO: 1733) CEP290-923 + GCUAAAUCAUGCAAGUGACCUA 22 upstream (SEQ ID NO: 1734) CEP290-924 + GUUUGUUCUGGGUACAGGGGUAA 23 upstream (SEQ ID NO: 1735) CEP290-925 + GUUCUGGGUACAGGGGUAA 19 upstream (SEQ ID NO: 1736) CEP290-926 + GACUCAUAAUUUAGUAGGAAUC 22 upstream (SEQ ID NO: 1737) CEP290-927 - GGAAUGGAUGUAGCCAACAGUAG 23 upstream (SEQ ID NO: 1738) CEP290-928 - GAAUGGAUGUAGCCAACAGUAG 22 upstream (SEQ ID NO: 1739) CEP290-929 - GGAUGUAGCCAACAGUAG 18 upstream (SEQ ID NO: 1740) CEP290-930 - GGUAGAAUAUUGUAAUCAAAGG 22 upstream (SEQ ID NO: 1741) CEP290-931 - GUAGAAUAUUGUAAUCAAAGG 21 upstream (SEQ ID NO: 1742) CEP290-932 - GAAUAUUGUAAUCAAAGG 18 upstream (SEQ ID NO: 1743) CEP290-933 + GGAACAAAAGCCAGGGACC 19 upstream (SEQ ID NO: 1744) CEP290-934 + GAACAAAAGCCAGGGACC 18 upstream (SEQ ID NO: 1745) CEP290-935 + GAAUUAGAUCUUAUUCUACUCCU 23 upstream (SEQ ID NO: 1746) CEP290-936 + GCCUAGGACUUUCUAAUGC 19 upstream (SEQ ID NO: 1747) CEP290-937 - GAUUUGUUCAUCUUCCUCAU 20 upstream (SEQ ID NO: 774) CEP290-938 - GAGAGGUGAUUAUGUUACUUUUUA 24 upstream (SEQ ID NO: 1749) CEP290-939 - GAGGUGAUUAUGUUACUUUUUA 22 upstream (SEQ ID NO: 1750) CEP290-940 - GGUGAUUAUGUUACUUUUUA 20 upstream (SEQ ID NO: 780) CEP290-941 - GUGAUUAUGUUACUUUUUA 19 upstream (SEQ ID NO: 1752) CEP290-942 - GUCCUAUCCUCUCCAGCAU 19 upstream (SEQ ID NO: 1753) CEP290-943 + GAUAAACAUGACUCAUAAUUUAG 23 upstream (SEQ ID NO: 1754) CEP290-944 - GGUAGAAUAUUGUAAUCAAAG 21 upstream (SEQ ID NO: 1755) CEP290-945 - GUAGAAUAUUGUAAUCAAAG 20 upstream (SEQ ID NO: 1756) CEP290-946 + GUUCUGGGUACAGGGGUAAGAGA 23 upstream (SEQ ID NO: 1757) CEP290-947 + GGGUACAGGGGUAAGAGA 18 upstream (SEQ ID NO: 1758) CEP290-948 + GUUUGUUCUGGGUACAGGGGU 21 upstream (SEQ ID NO: 1759) CEP290-949 - GUUUGCUUUCUGCUGCUUUUGCCA 24 upstream (SEQ ID NO: 1760) CEP290-950 - GCUUUCUGCUGCUUUUGCCA 20 upstream (SEQ ID NO: 776) CEP290-951 - GACAUCUAAGAGAAAAAGGAGC 22 upstream (SEQ ID NO: 1762) CEP290-952 + GGAGAGGAUAGGACAGAGGACA 22 upstream (SEQ ID NO: 1763) CEP290-953 + GAGAGGAUAGGACAGAGGACA 21 upstream (SEQ ID NO: 1764) CEP290-954 + GAGGAUAGGACAGAGGACA 19 upstream (SEQ ID NO: 1765) CEP290-955 + GGAAAGAUGAAAAAUACUCUU 21 upstream (SEQ ID NO: 1766) CEP290-956 + GAAAGAUGAAAAAUACUCUU 20 upstream (SEQ ID NO: 462) CEP290-957 + GGAAAGAUGAAAAAUACUCUUU 22 upstream (SEQ ID NO: 1767) CEP290-958 + GAAAGAUGAAAAAUACUCUUU 21 upstream (SEQ ID NO: 1768) CEP290-959 + GGAAAGAUGAAAAAUACUCU 20 upstream (SEQ ID NO: 778) CEP290-960 + GAAAGAUGAAAAAUACUCU 19 upstream (SEQ ID NO: 1770) CEP290-961 + GGAUAGGACAGAGGACAUGGAGAA 24 upstream (SEQ ID NO: 1771) CEP290-962 + GAUAGGACAGAGGACAUGGAGAA 23 upstream (SEQ ID NO: 1772) CEP290-963 + GGACAGAGGACAUGGAGAA 19 upstream (SEQ ID NO: 1773) CEP290-964 + GACAGAGGACAUGGAGAA 18 upstream (SEQ ID NO: 1774) CEP290-965 + GGAUAGGACAGAGGACAUGGAGA 23 upstream (SEQ ID NO: 1775) CEP290-966 + GAUAGGACAGAGGACAUGGAGA 22 upstream (SEQ ID NO: 1776) CEP290-967 + GGACAGAGGACAUGGAGA 18 upstream (SEQ ID NO: 1777) CEP290-968 + GGAACAAAAGCCAGGGACCAU 21 upstream (SEQ ID NO: 1778) CEP290-969 + GAACAAAAGCCAGGGACCAU 20 upstream (SEQ ID NO: 465) CEP290-970 + GUGUGUGUGUGUGUGUGUUAU 21 upstream (SEQ ID NO: 1779) CEP290-971 + GUGUGUGUGUGUGUGUUAU 19 upstream (SEQ ID NO: 1780) CEP290-972 + GUGUGUGUGUGUGUGUGUUAUG 22 upstream (SEQ ID NO: 1781) CEP290-973 + GUGUGUGUGUGUGUGUUAUG 20 upstream (SEQ ID NO: 1154) CEP290-974 + GUGUGUGUGUGUGUUAUG 18 upstream (SEQ ID NO: 1783) CEP290-975 + UACUGUUGGCUACAUCCAUUCC 22 upstream (SEQ ID NO: 1784) CEP290-976 + UGUUGGCUACAUCCAUUCC 19 upstream (SEQ ID NO: 1785) CEP290-977 + UUUACAGAGUGCAUCCAUGGUC 22 upstream (SEQ ID NO: 1786) CEP290-978 + UUACAGAGUGCAUCCAUGGUC 21 upstream (SEQ ID NO: 1787) CEP290-979 + UACAGAGUGCAUCCAUGGUC 20 upstream (SEQ ID NO: 1788) CEP290-980 - UCCAGCAUUAGAAAGUCCUAGGC 23 upstream (SEQ ID NO: 1789) CEP290-981 - UGGUCCCUGGCUUUUGUUCC 20 upstream (SEQ ID NO: 1790) CEP290-982 - UCAUAGAGACACAUUCAGUAA 21 upstream (SEQ ID NO: 1791) CEP290-983 - UAGAGACACAUUCAGUAA 18 upstream (SEQ ID NO: 1792) CEP290-984 - UCAAAAGCUUUUGCUGGCUCA 21 upstream (SEQ ID NO: 1793) CEP290-985 + UCCAUAAGCCUCUAUUUCUGAU 22 upstream (SEQ ID NO: 1794) CEP290-986 + UAAGCCUCUAUUUCUGAU 18 upstream (SEQ ID NO: 1795) CEP290-987 + UAAAUCAUGCAAGUGACCUA 20 upstream (SEQ ID NO: 508) CEP290-988 - UCUUUUAACCAGACAUCU 18 upstream (SEQ ID NO: 1796) CEP290-989 + UUUGUUCUGGGUACAGGGGUAA 22 upstream (SEQ ID NO: 1797) CEP290-990 + UUGUUCUGGGUACAGGGGUAA 21 upstream (SEQ ID NO: 1798) CEP290-991 + UGUUCUGGGUACAGGGGUAA 20 upstream (SEQ ID NO: 1799) CEP290-992 + UUCUGGGUACAGGGGUAA 18 upstream (SEQ ID NO: 1800) CEP290-993 + UGACUCAUAAUUUAGUAGGAAUC 23 upstream (SEQ ID NO: 1801) CEP290-994 + UCAUAAUUUAGUAGGAAUC 19 upstream (SEQ ID NO: 1802) CEP290-995 - UGGAAUGGAUGUAGCCAACAGUAG 24 upstream (SEQ ID NO: 1803) CEP290-996 - UGGAUGUAGCCAACAGUAG 19 upstream (SEQ ID NO: 1804) CEP290-997 + UCACCUCUCUUUGGCAAAAGCAG 23 upstream (SEQ ID NO: 1805) CEP290-998 + UCUCUUUGGCAAAAGCAG 18 upstream (SEQ ID NO: 1806) CEP290-999 - UAGAAUAUUGUAAUCAAAGG 20 upstream (SEQ ID NO: 1807) CEP290-1000 + UCCAAGGAACAAAAGCCAGGGACC 24 upstream (SEQ ID NO: 1808) CEP290-1001 + UCCAUUCCAAGGAACAAAAGC 21 upstream (SEQ ID NO: 1809) CEP290-1002 + UUAGAUCUUAUUCUACUCCU 20 upstream (SEQ ID NO: 902) CEP290-1003 + UAGAUCUUAUUCUACUCCU 19 upstream (SEQ ID NO: 1811) CEP290-1004 + UCUUGCCUAGGACUUUCUAAUGC 23 upstream (SEQ ID NO: 1812) CEP290-1005 + UUGCCUAGGACUUUCUAAUGC 21 upstream (SEQ ID NO: 1813) CEP290-1006 + UGCCUAGGACUUUCUAAUGC 20 upstream (SEQ ID NO: 632) CEP290-1007 - UCCUGAUUUGUUCAUCUUCCUCAU 24 upstream (SEQ ID NO: 1814) CEP290-1008 - UGAUUUGUUCAUCUUCCUCAU 21 upstream (SEQ ID NO: 1815) CEP290-1009 - UUUGUUCAUCUUCCUCAU 18 upstream (SEQ ID NO: 1816) CEP290-1010 - UGAUUAUGUUACUUUUUA 18 upstream (SEQ ID NO: 1817) CEP290-1011 - UCUUUUAACCAGACAUCUAA 20 upstream (SEQ ID NO: 1818) CEP290-1012 - UUUUAACCAGACAUCUAA 18 upstream (SEQ ID NO: 1819) CEP290-1013 - UCUGUCCUAUCCUCUCCAGCAU 22 upstream (SEQ ID NO: 1820) CEP290-1014 - UGUCCUAUCCUCUCCAGCAU 20 upstream (SEQ ID NO: 899) CEP290-1015 - UCCUAUCCUCUCCAGCAU 18 upstream (SEQ ID NO: 1822) CEP290-1016 + UGAUAAACAUGACUCAUAAUUUAG 24 upstream (SEQ ID NO: 1823) CEP290-1017 + UAAACAUGACUCAUAAUUUAG 21 upstream (SEQ ID NO: 1824) CEP290-1018 - UAGAAUAUUGUAAUCAAAG 19 upstream (SEQ ID NO: 1825) CEP290-1019 + UGUUCUGGGUACAGGGGUAAGAGA 24 upstream (SEQ ID NO: 1826) CEP290-1020 + UUCUGGGUACAGGGGUAAGAGA 22 upstream (SEQ ID NO: 1827) CEP290-1021 + UCUGGGUACAGGGGUAAGAGA 21 upstream (SEQ ID NO: 1828) CEP290-1022 + UGGGUACAGGGGUAAGAGA 19 upstream (SEQ ID NO: 1829) CEP290-1023 + UAGUUUGUUCUGGGUACAGGGGU 23 upstream (SEQ ID NO: 1830) CEP290-1024 + UUUGUUCUGGGUACAGGGGU 20 upstream (SEQ ID NO: 1831) CEP290-1025 + UUGUUCUGGGUACAGGGGU 19 upstream (SEQ ID NO: 1832) CEP290-1026 + UGUUCUGGGUACAGGGGU 18 upstream (SEQ ID NO: 1833) CEP290-1027 - UUUGCUUUCUGCUGCUUUUGCCA 23 upstream (SEQ ID NO: 1834) CEP290-1028 + UUGCUUUCUGCUGCUUUUGCCA 22 upstream (SEQ ID NO: 1835) CEP290-1029 + UGCUUUCUGCUGCUUUUGCCA 21 upstream (SEQ ID NO: 1836) CEP290-1030 + UUUCUGCUGCUUUUGCCA 18 upstream (SEQ ID NO: 1837) CEP290-1031 + UCUAAGAGAAAAAGGAGC 18 upstream (SEQ ID NO: 1838) CEP290-1032 + UGGAGAGGAUAGGACAGAGGACA 23 upstream (SEQ ID NO: 1839) CEP290-1033 + UUAGGAAAGAUGAAAAAUACUCUU 24 upstream (SEQ ID NO: 1840) CEP290-1034 + UAGGAAAGAUGAAAAAUACUCUU 23 upstream (SEQ ID NO: 1841) CEP290-1035 + UAGGAAAGAUGAAAAAUACUCUUU 24 upstream (SEQ ID NO: 1842) CEP290-1036 + UUUAGGAAAGAUGAAAAAUACUCU 24 upstream (SEQ ID NO: 1843) CEP290-1037 + UUAGGAAAGAUGAAAAAUACUCU 23 upstream  (SEQ ID NO: 1844) CEP290-1038 + UAGGAAAGAUGAAAAAUACUCU 22 upstream (SEQ ID NO: 1845) CEP290-1039 + UAGGACAGAGGACAUGGAGAA 21 upstream (SEQ ID NO: 1846) CEP290-1040 + UAGGACAGAGGACAUGGAGA 20 upstream (SEQ ID NO: 881) CEP290-1041 + UUUAUUCUACAAUAAAAAAUG 21 upstream (SEQ ID NO: 1848) CEP290-1042 + UUAUUCUACAAUAAAAAAUG 20 upstream (SEQ ID NO: 1849) CEP290-1043 + UAUUCUACAAUAAAAAAUG 19 upstream (SEQ ID NO: 1850) CEP290-1044 + UUGUGUGUGUGUGUGUGUGUUAU 23 upstream (SEQ ID NO: 1851) CEP290-1045 + UGUGUGUGUGUGUGUGUGUUAU 22 upstream (SEQ ID NO: 1852) CEP290-1046 + UGUGUGUGUGUGUGUGUUAU 20 upstream (SEQ ID NO: 1853) CEP290-1047 + UGUGUGUGUGUGUGUUAU 18 upstream (SEQ ID NO: 1854) CEP290-1048 + UUGUGUGUGUGUGUGUGUGUUAUG 24 upstream (SEQ ID NO: 1855) CEP290-1049 + UGUGUGUGUGUGUGUGUGUUAUG 23 upstream (SEQ ID NO: 1856) CEP290-1050 + UGUGUGUGUGUGUGUGUUAUG 21 upstream (SEQ ID NO: 1857) CEP290-1051 + UGUGUGUGUGUGUGUUAUG 19 upstream (SEQ ID NO: 1858) CEP290-1052 + ACUGUUGGCUACAUCCAUUCCA 22 upstream (SEQ ID NO: 1859) CEP290-1053 + AUUAUCCACAAGAUGUCUCUUGCC 24 upstream (SEQ ID NO: 1860) CEP290-1054 + AUCCACAAGAUGUCUCUUGCC 21 upstream (SEQ ID NO: 1861) CEP290-1055 + AUGAGCCAGCAAAAGCUU 18 upstream (SEQ ID NO: 1862) CEP290-1056 + ACAGAGUGCAUCCAUGGUCCAGG 23 upstream (SEQ ID NO: 1863) CEP290-1057 + AGAGUGCAUCCAUGGUCCAGG 21 upstream (SEQ ID NO: 1864) CEP290-1058 + AGUGCAUCCAUGGUCCAGG 19 upstream (SEQ ID NO: 1865) CEP290-1059 - AGCUGAAAUAUUAAGGGCUCUUC 23 upstream (SEQ ID NO: 1866) CEP290-1060 - AAAUAUUAAGGGCUCUUC 18 upstream (SEQ ID NO: 1867) CEP290-1061 - AACUCUAUACCUUUUACUGAGGA 23 upstream (SEQ ID NO: 1868) CEP290-1062 - ACUCUAUACCUUUUACUGAGGA 22 upstream (SEQ ID NO: 1869) CEP290-1063 - ACUUGAACUCUAUACCUUUUACU 23 upstream (SEQ ID NO: 1870) CEP290-1064 - AACUCUAUACCUUUUACU 18 upstream (SEQ ID NO: 1871) CEP290-1065 + AGUAGGAAUCCUGAAAGCUACU 22 upstream (SEQ ID NO: 1872) CEP290-1066 + AGGAAUCCUGAAAGCUACU 19 upstream (SEQ ID NO: 1873) CEP290-1067 - AGCCAACAGUAGCUGAAAUAUU 22 upstream (SEQ ID NO: 1874) CEP290-1068 - AACAGUAGCUGAAAUAUU 18 upstream (SEQ ID NO: 1875) CEP290-1069 + AUCCAUUCCAAGGAACAAAAGCC 23 upstream (SEQ ID NO: 1876) CEP290-1070 + AUUCCAAGGAACAAAAGCC 19 upstream (SEQ ID NO: 1877) CEP290-1071 - AUCCCUUUCUCUUACCCCUGUACC 24 upstream (SEQ ID NO: 1878) CEP290-1072 + AGGACUUUCUAAUGCUGGAGAGGA 24 upstream (SEQ ID NO: 1879) CEP290-1073 + ACUUUCUAAUGCUGGAGAGGA 21 upstream (SEQ ID NO: 1880) CEP290-1074 + AAUGCUGGAGAGGAUAGGACA 21 upstream (SEQ ID NO: 1881) CEP290-1075 + AUGCUGGAGAGGAUAGGACA 20 upstream (SEQ ID NO: 838) CEP290-1076 + AUCAUAAGUUACAAUCUGUGAAU 23 upstream (SEQ ID NO: 1883) CEP290-1077 + AUAAGUUACAAUCUGUGAAU 20 upstream (SEQ ID NO: 1884) CEP290-1078 + AAGUUACAAUCUGUGAAU 18 upstream (SEQ ID NO: 1885) CEP290-1079 + AACCAGACAUCUAAGAGAAAA 21 upstream (SEQ ID NO: 1886) CEP290-1080 + ACCAGACAUCUAAGAGAAAA 20 upstream (SEQ ID NO: 1087) CEP290-1081 + AAGCCUCUAUUUCUGAUGAGGAAG 24 upstream (SEQ ID NO: 1888) CEP290-1082 + AGCCUCUAUUUCUGAUGAGGAAG 23 upstream (SEQ ID NO: 1889) CEP290-1083 + AUGAGGAAGAUGAACAAAUC 20 upstream (SEQ ID NO: 733) CEP290-1084 + AUUUACUGAAUGUGUCUCU 19 upstream (SEQ ID NO: 1891) CEP290-1085 + ACAGGGGUAAGAGAAAGGG 19 upstream (SEQ ID NO: 1892) CEP290-1086 + CUACUGUUGGCUACAUCCAUUCCA 24 upstream (SEQ ID NO: 1893) CEP290-1087 + CUGUUGGCUACAUCCAUUCCA 21 upstream (SEQ ID NO: 1894) CEP290-1088 + CCACAAGAUGUCUCUUGCC 19 upstream (SEQ ID NO: 1895) CEP290-1089 + CACAAGAUGUCUCUUGCC 18 upstream (SEQ ID NO: 1896) CEP290-1090 + CCUUUGUAGUUAUCUUACAGCCAC 24 upstream (SEQ ID NO: 1897) CEP290-1091 + CUUUGUAGUUAUCUUACAGCCAC 23 upstream (SEQ ID NO: 1898) CEP290-1092 + CUCUAUGAGCCAGCAAAAGCUU 22 upstream (SEQ ID NO: 1899) CEP290-1093 + CUAUGAGCCAGCAAAAGCUU 20 upstream (SEQ ID NO: 748) CEP290-1094 + CAGAGUGCAUCCAUGGUCCAGG 22 upstream (SEQ ID NO: 1901) CEP290-1095 + CUGAAAUAUUAAGGGCUCUUC 21 upstream (SEQ ID NO: 1902) CEP290-1096 + CUCUAUACCUUUUACUGAGGA 21 upstream (SEQ ID NO: 1903) CEP290-1097 - CUAUACCUUUUACUGAGGA 19 upstream (SEQ ID NO: 1904) CEP290-1098 - CACUUGAACUCUAUACCUUUUACU 24 upstream (SEQ ID NO: 1905) CEP290-1099 - CUUGAACUCUAUACCUUUUACU 22 upstream (SEQ ID NO: 1906) CEP290-1100 - CCAACAGUAGCUGAAAUAUU 20 upstream (SEQ ID NO: 1907) CEP290-1101 - CAACAGUAGCUGAAAUAUU 19 upstream (SEQ ID NO: 1908) CEP290-1102 + CAUCCAUUCCAAGGAACAAAAGCC 24 upstream (SEQ ID NO: 1909) CEP290-1103 + CCAUUCCAAGGAACAAAAGCC 21 upstream (SEQ ID NO: 1910) CEP290-1104 + CAUUCCAAGGAACAAAAGCC 20 upstream (SEQ ID NO: 1131) CEP290-1105 - CCCUUUCUCUUACCCCUGUACC 22 upstream (SEQ ID NO: 1912) CEP290-1106 - CCUUUCUCUUACCCCUGUACC 21 upstream (SEQ ID NO: 1913) CEP290-1107 - CUUUCUCUUACCCCUGUACC 20 upstream (SEQ ID NO: 1914) CEP290-1108 + CUUUCUAAUGCUGGAGAGGA 20 upstream (SEQ ID NO: 869) CEP290-1109 + CUAAUGCUGGAGAGGAUAGGACA 23 upstream (SEQ ID NO: 1916) CEP290-1110 - CAUAAGUUACAAUCUGUGAAU 21 upstream (SEQ ID NO: 1917) CEP290-1111 - CCAGACAUCUAAGAGAAAA 19 upstream (SEQ ID NO: 1918) CEP290-1112 - CAGACAUCUAAGAGAAAA 18 upstream (SEQ ID NO: 1919) CEP290-1113 + CCUCUAUUUCUGAUGAGGAAG 21 upstream (SEQ ID NO: 1920) CEP290-1114 + CUCUAUUUCUGAUGAGGAAG 20 upstream (SEQ ID NO: 866) CEP290-1115 + CUAUUUCUGAUGAGGAAG 18 upstream (SEQ ID NO: 1922) CEP290-1116 + CUGAUGAGGAAGAUGAACAAAUC 23 upstream (SEQ ID NO: 1923) CEP290-1117 + CAUUUACUGAAUGUGUCUCU 20 upstream (SEQ ID NO: 856) CEP290-1118 + CAGGGGUAAGAGAAAGGG 18 upstream (SEQ ID NO: 1925) CEP290-1119 + GUUGGCUACAUCCAUUCCA 19 upstream (SEQ ID NO: 1926) CEP290-1120 - GUAGUUAUCUUACAGCCAC 19 upstream (SEQ ID NO: 1927) CEP290-1121 + GUCUCUAUGAGCCAGCAAAAGCUU 24 upstream (SEQ ID NO: 1928) CEP290-1122 + GAGUGCAUCCAUGGUCCAGG 20 upstream (SEQ ID NO: 1929) CEP290-1123 + GUGCAUCCAUGGUCCAGG 18 upstream (SEQ ID NO: 1930) CEP290-1124 - GCUGAAAUAUUAAGGGCUCUUC 22 upstream (SEQ ID NO: 1931) CEP290-1125 - GAAAUAUUAAGGGCUCUUC 19 upstream (SEQ ID NO: 1932) CEP290-1126 - GAACUCUAUACCUUUUACUGAGGA 24 upstream (SEQ ID NO: 1933) CEP290-1127 - GAACUCUAUACCUUUUACU 19 upstream (SEQ ID NO: 1934) CEP290-1128 + GUAGGAAUCCUGAAAGCUACU 21 upstream (SEQ ID NO: 1935) CEP290-1129 + GGAAUCCUGAAAGCUACU 18 upstream (SEQ ID NO: 1936) CEP290-1130 - GUAGCCAACAGUAGCUGAAAUAUU 24 upstream (SEQ ID NO: 1937) CEP290-1131 - GCCAACAGUAGCUGAAAUAUU 21 upstream (SEQ ID NO: 1938) CEP290-1132 + GGACUUUCUAAUGCUGGAGAGGA 23 upstream (SEQ ID NO: 1939) CEP290-1133 + GACUUUCUAAUGCUGGAGAGGA 22 upstream (SEQ ID NO: 1940) CEP290-1134 + GCUGGAGAGGAUAGGACA 18 upstream (SEQ ID NO: 1941) CEP290-1135 + GCCUCUAUUUCUGAUGAGGAAG 22 upstream (SEQ ID NO: 1942) CEP290-1136 + GAUGAGGAAGAUGAACAAAUC 21 upstream (SEQ ID NO: 1943) CEP290-1137 + GAGGAAGAUGAACAAAUC 18 upstream (SEQ ID NO: 1944) CEP290-1138 + GGGUACAGGGGUAAGAGAAAGGG 23 upstream (SEQ ID NO: 1945) CEP290-1139 + GGUACAGGGGUAAGAGAAAGGG 22 upstream (SEQ ID NO: 1946) CEP290-1140 + GUACAGGGGUAAGAGAAAGGG 21 upstream (SEQ ID NO: 1947) CEP290-1141 + GUGUGUGUGUGUGUGUGUUAUGU 23 upstream (SEQ ID NO: 1948) CEP290-1142 + GUGUGUGUGUGUGUGUUAUGU 21 upstream (SEQ ID NO: 1949) CEP290-1143 + GUGUGUGUGUGUGUUAUGU 19 upstream (SEQ ID NO: 1950) CEP290-1144 + UACUGUUGGCUACAUCCAUUCCA 23 upstream (SEQ ID NO: 1951) CEP290-1145 + UGUUGGCUACAUCCAUUCCA 20 upstream (SEQ ID NO: 1952) CEP290-1146 + UUGGCUACAUCCAUUCCA 18 upstream (SEQ ID NO: 1953) CEP290-1147 + UUAUCCACAAGAUGUCUCUUGCC 23 upstream (SEQ ID NO: 1954) CEP290-1148 + UAUCCACAAGAUGUCUCUUGCC 22 upstream (SEQ ID NO: 1955) CEP290-1149 + UCCACAAGAUGUCUCUUGCC 20 upstream (SEQ ID NO: 885) CEP290-1150 - UUUGUAGUUAUCUUACAGCCAC 22 upstream (SEQ ID NO: 1957) CEP290-1151 - UUGUAGUUAUCUUACAGCCAC 21 upstream (SEQ ID NO: 1958) CEP290-1152 - UGUAGUUAUCUUACAGCCAC 20 upstream (SEQ ID NO: 1959) CEP290-1153 - UAGUUAUCUUACAGCCAC 18 upstream (SEQ ID NO: 1960) CEP290-1154 + UCUCUAUGAGCCAGCAAAAGCUU 23 upstream (SEQ ID NO: 1961) CEP290-1155 + UCUAUGAGCCAGCAAAAGCUU 21 upstream (SEQ ID NO: 1962) CEP290-1156 + UAUGAGCCAGCAAAAGCUU 19 upstream (SEQ ID NO: 1963) CEP290-1157 + UACAGAGUGCAUCCAUGGUCCAGG 24 upstream (SEQ ID NO: 1964) CEP290-1158 - UAGCUGAAAUAUUAAGGGCUCUUC 24 upstream (SEQ ID NO: 1965) CEP290-1159 - UGAAAUAUUAAGGGCUCUUC 20 upstream (SEQ ID NO: 1966) CEP290-1160 - UCUAUACCUUUUACUGAGGA 20 upstream (SEQ ID NO: 889) CEP290-1161 - UAUACCUUUUACUGAGGA 18 upstream (SEQ ID NO: 1968) CEP290-1162 - UUGAACUCUAUACCUUUUACU 21 upstream (SEQ ID NO: 1969) CEP290-1163 - UGAACUCUAUACCUUUUACU 20 upstream (SEQ ID NO: 1970) CEP290-1164 + UUAGUAGGAAUCCUGAAAGCUACU 24 upstream (SEQ ID NO: 1971) CEP290-1165 + UAGUAGGAAUCCUGAAAGCUACU 23 upstream (SEQ ID NO: 1972) CEP290-1166 + UAGGAAUCCUGAAAGCUACU 20 upstream (SEQ ID NO: 760) CEP290-1167 - UAGCCAACAGUAGCUGAAAUAUU 23 upstream (SEQ ID NO: 1974) CEP290-1168 + UCCAUUCCAAGGAACAAAAGCC 22 upstream (SEQ ID NO: 1975) CEP290-1169 + UUCCAAGGAACAAAAGCC 18 upstream (SEQ ID NO: 1976) CEP290-1170 - UCCCUUUCUCUUACCCCUGUACC 23 upstream (SEQ ID NO: 1977) CEP290-1171 - UUUCUCUUACCCCUGUACC 19 upstream (SEQ ID NO: 1978) CEP290-1172 - UUCUCUUACCCCUGUACC 18 upstream (SEQ ID NO: 1979) CEP290-1173 + UUUCUAAUGCUGGAGAGGA 19 upstream (SEQ ID NO: 1980) CEP290-1174 + UUCUAAUGCUGGAGAGGA 18 upstream (SEQ ID NO: 1981) CEP290-1175 + UCUAAUGCUGGAGAGGAUAGGACA 24 upstream (SEQ ID NO: 1982) CEP290-1176 + UAAUGCUGGAGAGGAUAGGACA 22 upstream (SEQ ID NO: 1983) CEP290-1177 + UGCUGGAGAGGAUAGGACA 19 upstream (SEQ ID NO: 1984) CEP290-1178 - UAUCAUAAGUUACAAUCUGUGAAU 24 upstream (SEQ ID NO: 1985) CEP290-1179 - UCAUAAGUUACAAUCUGUGAAU 22 upstream (SEQ ID NO: 1986) CEP290-1180 - UAAGUUACAAUCUGUGAAU 19 upstream (SEQ ID NO: 1987) CEP290-1181 - UUUAACCAGACAUCUAAGAGAAAA 24 upstream (SEQ ID NO: 1988) CEP290-1182 - UUAACCAGACAUCUAAGAGAAAA 23 upstream (SEQ ID NO: 1989) CEP290-1183 - UAACCAGACAUCUAAGAGAAAA 22 upstream (SEQ ID NO: 1990) CEP290-1184 + UCUAUUUCUGAUGAGGAAG 19 upstream (SEQ ID NO: 1991) CEP290-1185 + UCUGAUGAGGAAGAUGAACAAAUC 24 upstream (SEQ ID NO: 1992) CEP290-1186 + UGAUGAGGAAGAUGAACAAAUC 22 upstream (SEQ ID NO: 1993) CEP290-1187 + UGAGGAAGAUGAACAAAUC 19 upstream (SEQ ID NO: 1994) CEP290-1188 + UUUUCAUUUACUGAAUGUGUCUCU 24 upstream (SEQ ID NO: 1995) CEP290-1189 + UUUCAUUUACUGAAUGUGUCUCU 23 upstream (SEQ ID NO: 1996) CEP290-1190 + UUCAUUUACUGAAUGUGUCUCU 22 upstream (SEQ ID NO: 1997) CEP290-1191 + UCAUUUACUGAAUGUGUCUCU 21 upstream (SEQ ID NO: 1998) CEP290-1192 + UUUACUGAAUGUGUCUCU 18 upstream (SEQ ID NO: 1999) CEP290-1193 + UGGGUACAGGGGUAAGAGAAAGGG 24 upstream (SEQ ID NO: 2000) CEP290-1194 + UACAGGGGUAAGAGAAAGGG 20 upstream (SEQ ID NO: 2001) CEP290-1195 + UGUGUGUGUGUGUGUGUGUUAUGU 24 upstream (SEQ ID NO: 2002) CEP290-1196 + UGUGUGUGUGUGUGUGUUAUGU 22 upstream (SEQ ID NO: 2003) CEP290-1197 + UGUGUGUGUGUGUGUUAUGU 20 upstream (SEQ ID NO: 1185) CEP290-1198 + UGUGUGUGUGUGUUAUGU 18 upstream (SEQ ID NO: 2005) CEP290-1199 + AUUUACAGAGUGCAUCCAUGGUCC 24 upstream (SEQ ID NO: 2006) CEP290-1200 + ACAGAGUGCAUCCAUGGUCC 20 upstream (SEQ ID NO: 1085) CEP290-1201 + AGAGUGCAUCCAUGGUCC 18 upstream (SEQ ID NO: 2008) CEP290-1202 - ACUUGAACUCUAUACCUUUUA 21 upstream (SEQ ID NO: 2009) CEP290-1203 + AGCUAAAUCAUGCAAGUGACCU 22 upstream (SEQ ID NO: 2010) CEP290-1204 + AAAUCAUGCAAGUGACCU 18 upstream (SEQ ID NO: 2011) CEP290-1205 + AUCCAUAAGCCUCUAUUUCUGAUG 24 upstream (SEQ ID NO: 2012) CEP290-1206 + AUAAGCCUCUAUUUCUGAUG 20 upstream  (SEQ ID NO: 723) CEP290-1207 + AAGCCUCUAUUUCUGAUG 18 upstream (SEQ ID NO: 2014) CEP290-1208 + AGAAUAGUUUGUUCUGGGUA 20 upstream (SEQ ID NO: 2015) CEP290-1209 + AAUAGUUUGUUCUGGGUA 18 upstream (SEQ ID NO: 2016) CEP290-1210 + AGGAGAAUGAUCUAGAUAAUCAUU 24 upstream (SEQ ID NO: 2017) CEP290-1211 + AGAAUGAUCUAGAUAAUCAUU 21 upstream (SEQ ID NO: 2018) CEP290-1212 + AAUGAUCUAGAUAAUCAUU 19 upstream (SEQ ID NO: 2019) CEP290-1213 + AUGAUCUAGAUAAUCAUU 18 upstream (SEQ ID NO: 2020) CEP290-1214 + AAUGCUGGAGAGGAUAGGA 19 upstream (SEQ ID NO: 2021) CEP290-1215 + AUGCUGGAGAGGAUAGGA 18 upstream (SEQ ID NO: 2022) CEP290-1216 + AAAAUCCAUAAGCCUCUAUUUCUG 24 upstream (SEQ ID NO: 2023) CEP290-1217 + AAAUCCAUAAGCCUCUAUUUCUG 23 upstream (SEQ ID NO: 20241 CEP290-1218 + AAUCCAUAAGCCUCUAUUUCUG 22 upstream (SEQ ID NO: 2025) CEP290-1219 + AUCCAUAAGCCUCUAUUUCUG 21 upstream (SEQ ID NO: 2026) CEP290-1220 - AAACAGGUAGAAUAUUGUAAUCA 23 upstream (SEQ ID NO: 2027) CEP290-1221 - AACAGGUAGAAUAUUGUAAUCA 22 upstream (SEQ ID NO: 2028) CEP290-1222 - ACAGGUAGAAUAUUGUAAUCA 21 upstream (SEQ ID NO: 2029) CEP290-1223 - AGGUAGAAUAUUGUAAUCA 19 upstream (SEQ ID NO: 2030) CEP290-1224 + AAGGAACAAAAGCCAGGGACCA 22 upstream (SEQ ID NO: 2031) CEP290-1225 + AGGAACAAAAGCCAGGGACCA 21 upstream (SEQ ID NO: 2032) CEP290-1226 + AACAAAAGCCAGGGACCA 18 upstream (SEQ ID NO: 2033) CEP290-1227 - AGGUAGAAUAUUGUAAUCAAAGGA 24 upstream (SEQ ID NO: 2034) CEP290-1228 - AGAAUAUUGUAAUCAAAGGA 20 upstream (SEQ ID NO: 1089) CEP290-1229 - AAUAUUGUAAUCAAAGGA 18 upstream (SEQ ID NO: 2036) CEP290-1230 - AGUCAUGUUUAUCAAUAUUAUU 22 upstream (SEQ ID NO: 2037) CEP290-1231 - AUGUUUAUCAAUAUUAUU 18 upstream (SEQ ID NO: 2038) CEP290-1232 - AACCAGACAUCUAAGAGAAA 20 upstream (SEQ ID NO: 2039) CEP290-1233 - ACCAGACAUCUAAGAGAAA 19 upstream (SEQ ID NO: 2040) CEP290-1234 - AUUCUUAUCUAAGAUCCUUUCA 22 upstream (SEQ ID NO: 2041) CEP290-1235 - AAACAGGUAGAAUAUUGUAAUCAA 24 upstream (SEQ ID NO: 2042) CEP290-1236 - AACAGGUAGAAUAUUGUAAUCAA 23 upstream (SEQ ID NO: 2043) CEP290-1237 - ACAGGUAGAAUAUUGUAAUCAA 22 upstream (SEQ ID NO: 2044) CEP290-1238 - AGGUAGAAUAUUGUAAUCAA 20 upstream (SEQ ID NO: 1101) CEP290-1239 + AUGAGGAAGAUGAACAAAU 19 upstream (SEQ ID NO: 2046) CEP290-1240 + AGAGGAUAGGACAGAGGAC 19 upstream (SEQ ID NO: 2047) CEP290-1241 + CAGAGUGCAUCCAUGGUCC 19 upstream (SEQ ID NO: 2048) CEP290-1242 + CUUGCCUAGGACUUUCUAAUGCUG 24 upstream (SEQ ID NO: 2049) CEP290-1243 + CCUAGGACUUUCUAAUGCUG 20 upstream (SEQ ID NO: 858) CEP290-1244 + CUAGGACUUUCUAAUGCUG 19 upstream (SEQ ID NO: 2051) CEP290-1245 - CCACUUGAACUCUAUACCUUUUA 23 upstream (SEQ ID NO: 2052) CEP290-1246 - CACUUGAACUCUAUACCUUUUA 22 upstream (SEQ ID NO: 2053) CEP290-1247 - CUUGAACUCUAUACCUUUUA 20 upstream (SEQ ID NO: 2054) CEP290-1248 + CAGCUAAAUCAUGCAAGUGACCU 23 upstream (SEQ ID NO: 2055) CEP290-1249 + CUAAAUCAUGCAAGUGACCU 20 upstream (SEQ ID NO: 2056) CEP290-1250 + CUCUUGCCUAGGACUUUCUAAUG 23 upstream (SEQ ID NO: 2057) CEP290-1251 + CUUGCCUAGGACUUUCUAAUG 21 upstream (SEQ ID NO: 2058) CEP290-1252 + CCAUAAGCCUCUAUUUCUGAUG 22 upstream (SEQ ID NO: 2059) CEP290-1253 + CAUAAGCCUCUAUUUCUGAUG 21 upstream (SEQ ID NO: 2060) CEP290-1254 + CUAAUGCUGGAGAGGAUAGGA 21 upstream (SEQ ID NO: 2061) CEP290-1255 + CCAUAAGCCUCUAUUUCUG 19 upstream (SEQ ID NO: 2062) CEP290-1256 + CAUAAGCCUCUAUUUCUG 18 upstream (SEQ ID NO: 2063) CEP290-1257 - CAGGUAGAAUAUUGUAAUCA 20 upstream (SEQ ID NO: 2064) CEP290-1258 - CUUUCUGCUGCUUUUGCCAAA 21 upstream (SEQ ID NO: 2065) CEP290-1259 + CCAAGGAACAAAAGCCAGGGACCA 24 upstream (SEQ ID NO: 2066) CEP290-1260 + CAAGGAACAAAAGCCAGGGACCA 23 upstream (SEQ ID NO: 2067) CEP290-1261 + CUCUUAGAUGUCUGGUUAA 19 upstream (SEQ ID NO: 2068) CEP290-1262 - CAUGUUUAUCAAUAUUAUU 19 upstream (SEQ ID NO: 2069) CEP290-1263 - CCAGACAUCUAAGAGAAA 18 upstream (SEQ ID NO: 2070) CEP290-1264 - CUUAUCUAAGAUCCUUUCA 19 upstream (SEQ ID NO: 2071) CEP290-1265 - CAGGUAGAAUAUUGUAAUCAA 21 upstream (SEQ ID NO: 2072) CEP290-1266 + CUGAUGAGGAAGAUGAACAAAU 22 upstream (SEQ ID NO: 2073) CEP290-1267 + CUGGAGAGGAUAGGACAGAGGAC 23 upstream (SEQ ID NO: 2074) CEP290-1268 - CAUCUUCCUCAUCAGAAA 18 upstream (SEQ ID NO: 2075) CEP290-1269 + GCCUAGGACUUUCUAAUGCUG 21 upstream (SEQ ID NO: 2076) CEP290-1270 - GCCACUUGAACUCUAUACCUUUUA 24 upstream (SEQ ID NO: 2077) CEP290-1271 + GCUAAAUCAUGCAAGUGACCU 21 upstream (SEQ ID NO: 2078) CEP290-1272 + GCCUAGGACUUUCUAAUG 18 upstream (SEQ ID NO: 2079) CEP290-1273 + GGGAGAAUAGUUUGUUCUGGGUA 23 upstream (SEQ ID NO: 2080) CEP290-1274 + GGAGAAUAGUUUGUUCUGGGUA 22 upstream (SEQ ID NO: 2081) CEP290-1275 + GAGAAUAGUUUGUUCUGGGUA 21 upstream (SEQ ID NO: 2082) CEP290-1276 + GAAUAGUUUGUUCUGGGUA 19 upstream (SEQ ID NO: 2083) CEP290-1277 + GGAGAAUGAUCUAGAUAAUCAUU 23 upstream (SEQ ID NO: 2084) CEP290-1278 + GAGAAUGAUCUAGAUAAUCAUU 22 upstream (SEQ ID NO: 2085) CEP290-1279 + GAAUGAUCUAGAUAAUCAUU 20 upstream (SEQ ID NO: 2086) CEP290-1280 - GAAACAGGUAGAAUAUUGUAAUCA 24 upstream (SEQ ID NO: 2087) CEP290-1281 - GGUAGAAUAUUGUAAUCA 18 upstream (SEQ ID NO: 2088) CEP290-1282 - GCUUUCUGCUGCUUUUGCCAAA 22 upstream (SEQ ID NO: 2089) CEP290-1283 + GGAACAAAAGCCAGGGACCA 20 upstream (SEQ ID NO: 484) CEP290-1284 + GAACAAAAGCCAGGGACCA 19 upstream (SEQ ID NO: 2090) CEP290-1285 - GGUAGAAUAUUGUAAUCAAAGGA 23 upstream (SEQ ID NO: 2091) CEP290-1286 - GUAGAAUAUUGUAAUCAAAGGA 22 upstream (SEQ ID NO: 2092) CEP290-1287 - GAAUAUUGUAAUCAAAGGA 19 upstream (SEQ ID NO: 2093) CEP290-1288 - GAGUCAUGUUUAUCAAUAUUAUU 23 upstream (SEQ ID NO: 2094) CEP290-1289 - GUCAUGUUUAUCAAUAUUAUU 21 upstream (SEQ ID NO: 2095) CEP290-1290 - GGUAGAAUAUUGUAAUCAA 19 upstream (SEQ ID NO: 2096) CEP290-1291 - GUAGAAUAUUGUAAUCAA 18 upstream (SEQ ID NO: 2097) CEP290-1292 + GAUGAGGAAGAUGAACAAAU 20 upstream (SEQ ID NO: 773) CEP290-1293 + GCUGGAGAGGAUAGGACAGAGGAC 24 upstream (SEQ ID NO: 2099) CEP290-1294 + GGAGAGGAUAGGACAGAGGAC 21 upstream (SEQ ID NO: 2100) CEP290-1295 + GAGAGGAUAGGACAGAGGAC 20 upstream (SEQ ID NO: 772) CEP290-1296 + GAGGAUAGGACAGAGGAC 18 upstream (SEQ ID NO: 2102) CEP290-1297 - GUUCAUCUUCCUCAUCAGAAA 21 upstream (SEQ ID NO: 2103) CEP290-1298 + UUUACAGAGUGCAUCCAUGGUCC 23 upstream (SEQ ID NO: 2104) CEP290-1299 + UUACAGAGUGCAUCCAUGGUCC 22 upstream (SEQ ID NO: 2105) CEP290-1300 + UACAGAGUGCAUCCAUGGUCC 21 upstream (SEQ ID NO: 2106) CEP290-1301 + UUGCCUAGGACUUUCUAAUGCUG 23 upstream (SEQ ID NO: 2107) CEP290-1302 + UGCCUAGGACUUUCUAAUGCUG 22 upstream (SEQ ID NO: 2108) CEP290-1303 + UAGGACUUUCUAAUGCUG 18 upstream (SEQ ID NO: 2109) CEP290-1304 - UUGAACUCUAUACCUUUUA 19 upstream (SEQ ID NO: 2110) CEP290-1305 - UGAACUCUAUACCUUUUA 18 upstream (SEQ ID NO: 2111) CEP290-1306 + UCAGCUAAAUCAUGCAAGUGACCU 24 upstream (SEQ ID NO: 2112) CEP290-1307 + UAAAUCAUGCAAGUGACCU 19 upstream (SEQ ID NO: 2113) CEP290-1308 + UCUCUUGCCUAGGACUUUCUAAUG 24 upstream (SEQ ID NO: 2114) CEP290-1309 + UCUUGCCUAGGACUUUCUAAUG 22 upstream (SEQ ID NO: 2115) CEP290-1310 + UUGCCUAGGACUUUCUAAUG 20 upstream (SEQ ID NO: 906) CEP290-1311 + UGCCUAGGACUUUCUAAUG 19 upstream (SEQ ID NO: 2117) CEP290-1312 + UCCAUAAGCCUCUAUUUCUGAUG 23 upstream (SEQ ID NO: 2118) CEP290-1313 + UAAGCCUCUAUUUCUGAUG 19 upstream (SEQ ID NO: 2119) CEP290-1314 + UGGGAGAAUAGUUUGUUCUGGGUA 24 upstream (SEQ ID NO: 2120) CEP290-1315 + UUUCUAAUGCUGGAGAGGAUAGGA 24 upstream (SEQ ID NO: 2121) CEP290-1316 + UUCUAAUGCUGGAGAGGAUAGGA 23 upstream (SEQ ID NO: 2122) CEP290-1317 + UCUAAUGCUGGAGAGGAUAGGA 22 upstream (SEQ ID NO: 2123) CEP290-1318 + UAAUGCUGGAGAGGAUAGGA 20 upstream (SEQ ID NO: 873) CEP290-1319 + UCCAUAAGCCUCUAUUUCUG 20 upstream (SEQ ID NO: 886) CEP290-1320 - UUGCUUUCUGCUGCUUUUGCCAAA 24 upstream (SEQ ID NO: 2126) CEP290-1321 - UGCUUUCUGCUGCUUUUGCCAAA 23 upstream (SEQ ID NO: 2127) CEP290-1322 - UUUCUGCUGCUUUUGCCAAA 20 upstream (SEQ ID NO: 907) CEP290-1323 - UUCUGCUGCUUUUGCCAAA 19 upstream (SEQ ID NO: 2129) CEP290-1324 - UCUGCUGCUUUUGCCAAA 18 upstream (SEQ ID NO: 2130) CEP290-1325 - UAGAAUAUUGUAAUCAAAGGA 21 upstream (SEQ ID NO: 2131) CEP290-1326 + UUUUUCUCUUAGAUGUCUGGUUAA 24 upstream (SEQ ID NO: 2132) CEP290-1327 + UUUUCUCUUAGAUGUCUGGUUAA 23 upstream (SEQ ID NO: 2133) CEP290-1328 + UUUCUCUUAGAUGUCUGGUUAA 22 upstream (SEQ ID NO: 2134) CEP290-1329 + UUCUCUUAGAUGUCUGGUUAA 21 upstream (SEQ ID NO: 2135) CEP290-1330 + UCUCUUAGAUGUCUGGUUAA 20 upstream (SEQ ID NO: 2136) CEP290-1331 + UCUUAGAUGUCUGGUUAA 18 upstream (SEQ ID NO: 2137) CEP290-1332 - UGAGUCAUGUUUAUCAAUAUUAUU 24 upstream (SEQ ID NO: 2138) CEP290-1333 - UCAUGUUUAUCAAUAUUAUU 20 upstream (SEQ ID NO: 884) CEP290-1334 - UUUUAACCAGACAUCUAAGAGAAA 24 upstream (SEQ ID NO: 2140) CEP290-1335 - UUUAACCAGACAUCUAAGAGAAA 23 upstream (SEQ ID NO: 2141) CEP290-1336 - UUAACCAGACAUCUAAGAGAAA 22 upstream (SEQ ID NO: 2142) CEP290-1337 - UAACCAGACAUCUAAGAGAAA 21 upstream (SEQ ID NO: 2143) CEP290-1338 - UUAUUCUUAUCUAAGAUCCUUUCA 24 upstream (SEQ ID NO: 2144) CEP290-1339 - UAUUCUUAUCUAAGAUCCUUUCA 23 upstream (SEQ ID NO: 2145) CEP290-1340 - UUCUUAUCUAAGAUCCUUUCA 21 upstream (SEQ ID NO: 2146) CEP290-1341 - UCUUAUCUAAGAUCCUUUCA 20 upstream (SEQ ID NO: 892) CEP290-1342 - UUAUCUAAGAUCCUUUCA 18 upstream (SEQ ID NO: 2148) CEP290-1343 + UUCUGAUGAGGAAGAUGAACAAAU 24 upstream (SEQ ID NO: 2149) CEP290-1344 + UCUGAUGAGGAAGAUGAACAAAU 23 upstream (SEQ ID NO: 2150) CEP290-1345 + UGAUGAGGAAGAUGAACAAAU 21 upstream (SEQ ID NO: 2151) CEP290-1346 + UGAGGAAGAUGAACAAAU 18 upstream (SEQ ID NO: 2152) CEP290-1347 + UGGAGAGGAUAGGACAGAGGAC 22 upstream (SEQ ID NO: 2153) CEP290-1348 - UUUGUUCAUCUUCCUCAUCAGAAA 24 upstream (SEQ ID NO: 2154) CEP290-1349 - UUGUUCAUCUUCCUCAUCAGAAA 23 upstream (SEQ ID NO: 2155) CEP290-1350 - UGUUCAUCUUCCUCAUCAGAAA 22 upstream (SEQ ID NO: 2156) CEP290-1351 - UUCAUCUUCCUCAUCAGAAA 20 upstream (SEQ ID NO: 905) CEP290-1352 - UCAUCUUCCUCAUCAGAAA 19 upstream (SEQ ID NO: 2158) CEP290-1353 - ACUUACCUCAUGUCAUCUAGAGC 23 downstream (SEQ ID NO: 2159) CEP290-1354 - ACCUCAUGUCAUCUAGAGC 19 downstream (SEQ ID NO: 2160) CEP290-1355 + ACAGUUUUUAAGGCGGGGAGUCAC 24 downstream (SEQ ID NO: 2161) CEP290-1356 + AGUUUUUAAGGCGGGGAGUCAC 22 downstream (SEQ ID NO: 2162) CEP290-1357 - ACAGAGUUCAAGCUAAUAC 19 downstream (SEQ ID NO: 2163) CEP290-1358 + AUUAGCUUGAACUCUGUGCCAAAC 24 downstream (SEQ ID NO: 2164) CEP290-1359 + AGCUUGAACUCUGUGCCAAAC 21 downstream (SEQ ID NO: 2165) CEP290-1360 - AUGUGGUGUCAAAUAUGGUGCU 22 downstream (SEQ ID NO: 2166) CEP290-1361 - AUGUGGUGUCAAAUAUGGUGCUU 23 downstream (SEQ ID NO: 2167) CEP290-1362 + AGAUGACAUGAGGUAAGU 18 downstream (SEQ ID NO: 2168) CEP290-1363 - AAUACAUGAGAGUGAUUAGUGG 22 downstream (SEQ ID NO: 2169) CEP290-1364 - AUACAUGAGAGUGAUUAGUGG 21 downstream (SEQ ID NO: 2170) CEP290-1365 - ACAUGAGAGUGAUUAGUGG 19 downstream (SEQ ID NO: 2171) CEP290-16 + AAGACACUGCCAAUAGGGAUAGGU 24 downstream (SEQ ID NO: 1042) CEP290-1366 + AGACACUGCCAAUAGGGAUAGGU 23 downstream (SEQ ID NO: 1043) CEP290-1367 + ACACUGCCAAUAGGGAUAGGU 21 downstream (SEQ ID NO: 1044) CEP290-510 + ACUGCCAAUAGGGAUAGGU 19 downstream (SEQ ID NO: 1045) CEP290-1368 - AAAGGUUCAUGAGACUAGAGGUC 23 downstream (SEQ ID NO: 2176) CEP290-1369 - AAGGUUCAUGAGACUAGAGGUC 22 downstream (SEQ ID NO: 2177) CEP290-1370 - AGGUUCAUGAGACUAGAGGUC 21 downstream (SEQ ID NO: 2178) CEP290-1371 + AAACAGGAGAUACUCAACACA 21 downstream (SEQ ID NO: 2179) CEP290-1372 + AACAGGAGAUACUCAACACA 20 downstream (SEQ ID NO: 810) CEP290-1373 + ACAGGAGAUACUCAACACA 19 downstream (SEQ ID NO: 2181) CEP290-1374 + AGCACGUACAAAAGAACAUACAU 23 downstream (SEQ ID NO: 2182) CEP290-1375 + ACGUACAAAAGAACAUACAU 20 downstream (SEQ ID NO: 817) CEP290-1376 + AGUAAGGAGGAUGUAAGAC 19 downstream (SEQ ID NO: 2184) CEP290-1377 + AGCUUUUGACAGUUUUUAAGG 21 downstream (SEQ ID NO: 2185) CEP290-1378 - ACGUGCUCUUUUCUAUAUAU 20 downstream (SEQ ID NO: 622) CEP290-1379 + AAAUUCACUGAGCAAAACAACUGG 24 downstream (SEQ ID NO: 2186) CEP290-1380 + AAUUCACUGAGCAAAACAACUGG 23 downstream (SEQ ID NO: 2187) CEP290-1381 + AUUCACUGAGCAAAACAACUGG 22 downstream (SEQ ID NO: 2188) CEP290-1382 + ACUGAGCAAAACAACUGG 18 downstream (SEQ ID NO: 2189) CEP290-1383 + AACAAGUUUUGAAACAGGAA 20 downstream (SEQ ID NO: 809) CEP290-1384 + ACAAGUUUUGAAACAGGAA 19 downstream (SEQ ID NO: 2191) CEP290-1385 + AAUGCCUGAACAAGUUUUGAAA 22 downstream (SEQ ID NO: 2192) CEP290-1386 + AUGCCUGAACAAGUUUUGAAA 21 downstream (SEQ ID NO: 2193) CEP290-1387 + AUUCACUGAGCAAAACAACUGGAA 24 downstream (SEQ ID NO: 2194) CEP290-1388 + ACUGAGCAAAACAACUGGAA 20 downstream (SEQ ID NO: 819) CEP290-1389 + AAAAAGGUAAUGCCUGAACAAGUU 24 downstream (SEQ ID NO: 2196) CEP290-1390 + AAAAGGUAAUGCCUGAACAAGUU 23 downstream (SEQ ID NO: 2197) CEP290-1391 + AAAGGUAAUGCCUGAACAAGUU 22 downstream (SEQ ID NO: 2198) CEP290-1392 + AAGGUAAUGCCUGAACAAGUU 21 downstream (SEQ ID NO: 2199) CEP290-1393 + AGGUAAUGCCUGAACAAGUU 20 downstream (SEQ ID NO: 828) CEP290-1394 - ACGUGCUCUUULCUAUAUA 19 downstream (SEQ ID NO: 2201) CEP290-1395 + AUUAUCUAUUCCAUUCUUCACAC 23 downstream (SEQ ID NO: 2202) CEP290-1396 + AUCUAUUCCAUUCUUCACAC 20 downstream (SEQ ID NO: 2203) CEP290-1397 + AAGAGAGAAAUGGUUCCCUAUAUA 24 downstream (SEQ ID NO: 2204) CEP290-1398 + AGAGAGAAAUGGUUCCCUAUAUA 23 downstream (SEQ ID NO: 2205) CEP290-1399 + AGAGAAAUGGUUCCCUAUAUA 21 downstream (SEQ ID NO: 2206) CEP290-1400 + AGAAAUGGUUCCCUAUAUA 19 downstream (SEQ ID NO: 2207) CEP290-1401 - AGGAAAUUAUUGUUGCUUU 19 downstream (SEQ ID NO: 2208) CEP290-1402 + ACUGAGCAAAACAACUGGAAGA 22 downstream (SEQ ID NO: 2209) CEP290-1403 + AGCAAAACAACUGGAAGA 18 downstream (SEQ ID NO: 2210) CEP290-1404 + AUACAUAAGAAAGAACACUGUGGU 24 downstream (SEQ ID NO: 2211) CEP290-1405 + ACAUAAGAAAGAACACUGUGGU 22 downstream (SEQ ID NO: 2212) CEP290-1406 + AUAAGAAAGAACACUGUGGU 20 downstream (SEQ ID NO: 829) CEP290-1407 + AAGAAAGAACACUGUGGU 18 downstream (SEQ ID NO: 2214) CEP290-1408 - AAGAAUGGAAUAGAUAAU 18 downstream (SEQ ID NO: 2215) CEP290-1409 + AAGGAGGAUGUAAGACUGGAGA 22 downstream (SEQ ID NO: 2216) CEP290-1410 + AGGAGGAUGUAAGACUGGAGA 21 downstream (SEQ ID NO: 2217) CEP290-1411 + AGGAUGUAAGACUGGAGA 18 downstream (SEQ ID NO: 2218) CEP290-1412 - AAAAACUUGAAAUUUGAUAGUAG 23 downstream (SEQ ID NO: 2219) CEP290-1413 - AAAACUUGAAAUUUGAUAGUAG 22 downstream (SEQ ID NO: 2220) CEP290-1414 - AAACUUGAAAUUUGAUAGUAG 21 downstream (SEQ ID NO: 2221) CEP290-1415 - AACUUGAAAUUUGAUAGUAG 20 downstream (SEQ ID NO: 2222) CEP290-1416 - ACUUGAAAUUUGAUAGUAG 19 downstream (SEQ ID NO: 2223) CEP290-1417 - ACAUAUCUGUCUUCCUUA 18 downstream (SEQ ID NO: 2224) CEP290-1418 + AUUAAAAAAAGUAUGCUU 18 downstream (SEQ ID NO: 2225) CEP290-1419 + AUAUCAAAAGACUUAUAUUCCAUU 24 downstream (SEQ ID NO: 2226) CEP290-1420 + AUCAAAAGACUUAUAUUCCAUU 22 downstream (SEQ ID NO: 2227) CEP290-1421 + AAAAGACUUAUAUUCCAUU 19 downstream (SEQ ID NO: 2228) CEP290-1422 + AAAGACUUAUAUUCCAUU 18 downstream (SEQ ID NO: 2229) CEP290-1423 - AAAAUCAGAUUUCAUGUGUGAAGA 24 downstream (SEQ ID NO: 2230) CEP290-1424 - AAAUCAGAUUUCAUGUGUGAAGA 23 downstream (SEQ ID NO: 2231) CEP290-1425 - AAUCAGAUUUCAUGUGUGAAGA 22 downstream (SEQ ID NO: 2232) CEP290-1426 - AUCAGAUUUCAUGUGUGAAGA 21 downstream (SEQ ID NO: 2233) CEP290-1427 - AGAUUUCAUGUGUGAAGA 18 downstream (SEQ ID NO: 2234) CEP290-1428 - AAUGGAAUAUAAGUCUUUUGAUAU 24 downstream (SEQ ID NO: 2235) CEP290-1429 - AUGGAAUAUAAGUCUUUUGAUAU 23 downstream (SEQ ID NO: 2236) CEP290-1430 - AAUAUAAGUCUUUUGAUAU 19 downstream (SEQ ID NO: 2237) CEP290-1431 - AUAUAAGUCUUUUGAUAU 18 downstream (SEQ ID NO: 2238) CEP290-1432 - AAGAAUGGAAUAGAUAAUA 19 downstream (SEQ ID NO: 2239) CEP290-1433 - AGAAUGGAAUAGAUAAUA 18 downstream (SEQ ID NO: 2240) CEP290-1434 - AAAACUGGAUGGGUAAUAAAGCAA 24 downstream (SEQ ID NO: 2241) CEP290-1435 - AAACUGGAUGGGUAAUAAAGCAA 23 downstream (SEQ ID NO: 2242) CEP290-1436 - AACUGGAUGGGUAAUAAAGCAA 22 downstream (SEQ ID NO: 2243) CEP290-1437 - ACUGGAUGGGUAAUAAAGCAA 21 downstream (SEQ ID NO: 2244) CEP290-1438 + AUAGAAAUUCACUGAGCAAAACAA 24 downstream (SEQ ID NO: 2245) CEP290-1439 + AGAAAUUCACUGAGCAAAACAA 22 downstream (SEQ ID NO: 2246) CEP290-1440 + AAAUUCACUGAGCAAAACAA 20 downstream (SEQ ID NO: 808) CEP290-1441 + AAUUCACUGAGCAAAACAA 19 downstream (SEQ ID NO: 2248) CEP290-1442 + AUUCACUGAGCAAAACAA 18 downstream (SEQ ID NO: 2249) CEP290-1443 + AGGAUGUAAGACUGGAGAUAGAGA 24 downstream (SEQ ID NO: 2250) CEP290-1444 + AUGUAAGACUGGAGAUAGAGA 21 downstream (SEQ ID NO: 2251) CEP290-1445 - AAAUUUGAUAGUAGAAGAAAA 21 downstream (SEQ ID NO: 2252) CEP290-1446 - AAUUUGAUAGUAGAAGAAAA 20 downstream (SEQ ID NO: 2253) CEP290-1447 - AUUUGAUAGUAGAAGAAAA 19 downstream (SEQ ID NO: 2254) CEP290-1448 + AAAAUAAAACUAAGACACUGCCAA 24 downstream (SEQ ID NO: 1036) CEP290-1449 + AAAUAAAACUAAGACACUGCCAA 23 downstream (SEQ ID NO: 1037) CEP290-1450 + AAUAAAACUAAGACACUGCCAA 22 downstream (SEQ ID NO: 1038) CEP290-1451 + AUAAAACUAAGACACUGCCAA 21 downstream (SEQ ID NO: 1039) CEP290-1452 + AAAACUAAGACACUGCCAA 19 downstream (SEQ ID NO: 1040) CEP290-1453 + AAACUAAGACACUGCCAA 18 downstream (SEQ ID NO: 1041) CEP290-1454 - AAUAAAGCAAAAGAAAAAC 19 downstream (SEQ ID NO: 2261) CEP290-1455 - AUAAAGCAAAAGAAAAAC 18 downstream (SEQ ID NO: 2262) CEP290-1456 - AUUCUUUUUUUGUUGUUUUUUUUU 24 downstream (SEQ ID NO: 2263) CEP290-1457 + ACUCCAGCCUGGGCAACACA 20 downstream (SEQ ID NO: 2264) CEP290-1458 - CUUACCUCAUGUCAUCUAGAGC 22 downstream (SEQ ID NO: 2265) CEP290-1459 - CCUCAUGUCAUCUAGAGC 18 downstream (SEQ ID NO: 2266) CEP290-1460 + CAGUUUUUAAGGCGGGGAGUCAC 23 downstream (SEQ ID NO: 2267) CEP290-1461 - CACAGAGUUCAAGCUAAUAC 20 downstream (SEQ ID NO: 845) CEP290-1462 - CAGAGUUCAAGCUAAUAC 18 downstream (SEQ ID NO: 2269) CEP290-1463 + CUUGAACUCUGUGCCAAAC 19 downstream (SEQ ID NO: 2270) CEP290-1464 - CAUGUGGUGUCAAAUAUGGUGCU 23 downstream (SEQ ID NO: 2271) CEP290-1465 - CAUGUGGUGUCAAAUAUGGUGCUU 24 downstream (SEQ ID NO: 2272) CEP290-1466 + CUCUAGAUGACAUGAGGUAAGU 22 downstream (SEQ ID NO: 2273) CEP290-1467 + CUAGAUGACAUGAGGUAAGU 20 downstream (SEQ ID NO: 671) CEP290-1468 - CUAAUACAUGAGAGUGAUUAGUGG 24 downstream (SEQ ID NO: 2275) CEP290-1469 - CAUGAGAGUGAUUAGUGG 18 downstream (SEQ ID NO: 2276) CEP290-509 + CACUGCCAAUAGGGAUAGGU 20 downstream (SEQ ID NO: 613) CEP290-511 + CUGCCAAUAGGGAUAGGU 18 downstream (SEQ ID NO: 1046) CEP290-1470 + CCAAACAGGAGAUACUCAACACA 23 downstream (SEQ ID NO: 2278) CEP290-1471 + CAAACAGGAGAUACUCAACACA 22 downstream (SEQ ID NO: 2279) CEP290-1472 + CAGGAGAUACUCAACACA 18 downstream (SEQ ID NO: 2280) CEP290-1473 + CACGUACAAAAGAACAUACAU 21 downstream (SEQ ID NO: 2281) CEP290-1474 + CGUACAAAAGAACAUACAU 19 downstream (SEQ ID NO: 2282) CEP290-1475 + CAGUAAGGAGGAUGUAAGAC 20 downstream (SEQ ID NO: 676) CEP290-1476 + CUUUUGACAGUUUUUAAGG 19 downstream (SEQ ID NO: 2284) CEP290-1477 - CGUGCUCUUUUCUAUAUAU 19 downstream (SEQ ID NO: 2285) CEP290-1478 + CACUGAGCAAAACAACUGG 19 downstream (SEQ ID NO: 2286) CEP290-1479 + CCUGAACAAGULUUGAAACAGGAA 24 downstream (SEQ ID NO: 2287) CEP290-1480 + CUGAACAAGUUUUGAAACAGGAA 23 downstream (SEQ ID NO: 2288) CEP290-1481 + CAAGUUUUGAAACAGGAA 18 downstream (SEQ ID NO: 2289) CEP290-1482 + CCUGAACAAGUUUUGAAA 18 downstream (SEQ ID NO: 2290) CEP290-1483 + CACUGAGCAAAACAACUGGAA 21 downstream (SEQ ID NO: 2291) CEP290-1484 + CUGAGCAAAACAACUGGAA 19 downstream (SEQ ID NO: 2292) CEP290-1485 - CGUGCUCUUUUCUAUAUA 18 downstream (SEQ ID NO: 2293) CEP290-1486 + CUAUUCCAUUCUUCACAC 18 downstream (SEQ ID NO: 2294) CEP290-1487 - CUUAGGAAAUUAUUGUUGCUUU 22 downstream (SEQ ID NO: 2295) CEP290-1488 - CUUUUUGAGAGGUAAAGGUUC 21 downstream (SEQ ID NO: 2296) CEP290-1489 + CACUGAGCAAAACAACUGGAAGA 23 downstream (SEQ ID NO: 2297) CEP290-1490 + CUGAGCAAAACAACUGGAAGA 21 downstream (SEQ ID NO: 2298) CEP290-1491 + CAUAAGAAAGAACACUGUGGU 21 downstream (SEQ ID NO: 2299) CEP290-1492 - CUUGAAAUUUGAUAGUAG 18 downstream (SEQ ID NO: 2300) CEP290-1493 + CCAUUAAAAAAAGUAUGCUU 20 downstream (SEQ ID NO: 857) CEP290-1494 + CAUUAAAAAAAGUAUGCUU 19 downstream (SEQ ID NO: 2302) CEP290-1495 + CAAAAGACUUAUAUUCCAUU 20 downstream (SEQ ID NO: 842) CEP290-1496 - CAGAUUUCAUGUGUGAAGA 19 downstream (SEQ ID NO: 2304) CEP290-1497 - CUGGAUGGGUAAUAAAGCAA 20 downstream (SEQ ID NO: 2305) CEP290-1498 - CUUAAGCAUACUUUUUUUA 19 downstream (SEQ ID NO: 2306) CEP290-1499 - CUUUUUUUGUUGUUUUUUUUU 21 downstream (SEQ ID NO: 2307) CEP290-1500 + CUGCACUCCAGCCUGGGCAACACA 24 downstream (SEQ ID NO: 2308) CEP290-1501 + CACUCCAGCCUGGGCAACACA 21 downstream (SEQ ID NO: 2309) CEP290-1502 + CUCCAGCCUGGGCAACACA 19 downstream (SEQ ID NO: 2310) CEP290-1503 + GUUUUUAAGGCGGGGAGUCAC 21 downstream (SEQ ID NO: 2311) CEP290-230 - GGCACAGAGUUCAAGCUAAUAC 22 downstream (SEQ ID NO: 2312) CEP290-1504 - GCACAGAGUUCAAGCUAAUAC 21 downstream (SEQ ID NO: 2313) CEP290-1505 + GCUUGAACUCUGUGCCAAAC 20 downstream (SEQ ID NO: 461) CEP290-139 - GCAUGUGGUGUCAAAUAUGGUGCU 24 downstream (SEQ ID NO: 2314) CEP290-1506 - GUGGUGUCAAAUAUGGUGCU 20 downstream (SEQ ID NO: 782) CEP290-1507 - GGUGUCAAAUAUGGUGCU 18 downstream (SEQ ID NO: 2316) CEP290-1508 - GUGGUGUCAAAUAUGGUGCUU 21 downstream (SEQ ID NO: 2317) CEP290-1509 - GGUGUCAAAUAUGGUGCUU 19 downstream (SEQ ID NO: 2318) CEP290-1510 - GUGUCAAAUAUGGUGCUU 18 downstream (SEQ ID NO: 2319) CEP290-1511 + GCUCUAGAUGACAUGAGGUAAGU 23 downstream (SEQ ID NO: 2320) CEP290-11 + GACACUGCCAAUAGGGAUAGGU 22 downstream (SEQ ID NO: 1047) CEP290-1512 - GGUUCAUGAGACUAGAGGUC 20 downstream (SEQ ID NO: 2322) CEP290-1513 - GUUCAUGAGACUAGAGGUC 19 downstream (SEQ ID NO: 2323) CEP290-1514 + GCCAAACAGGAGAUACUCAACACA 24 downstream (SEQ ID NO: 2324) CEP290-1515 + GAGCACGUACAAAAGAACAUACAU 24 downstream (SEQ ID NO: 2325) CEP290-1516 + GCACGUACAAAAGAACAUACAU 22 downstream (SEQ ID NO: 2326) CEP290-1517 + GUACAAAAGAACAUACAU 18 downstream (SEQ ID NO: 2327) CEP290-1518 + GUGGCAGUAAGGAGGAUGUAAGAC 24 downstream (SEQ ID NO: 2328) CEP290-1519 + GGCAGUAAGGAGGAUGUAAGAC 22 downstream (SEQ ID NO: 2329) CEP290-1520 + GCAGUAAGGAGGAUGUAAGAC 21 downstream (SEQ ID NO: 2330) CEP290-1521 + GUAAGGAGGAUGUAAGAC 18 downstream (SEQ ID NO: 2331) CEP290-1522 + GGUAGCUUUUGACAGUUUUUAAGG 24 downstream (SEQ ID NO: 2332) CEP290-1523 + GUAGCUUUUGACAGUUUUUAAGG 23 downstream (SEQ ID NO: 2333) CEP290-1524 + GCUUUUGACAGUUUUUAAGG 20 downstream (SEQ ID NO: 482) CEP290-1525 - GUACGUGCUCUUUUCUAUAUAU 22 downstream (SEQ ID NO: 2334) CEP290-1526 - GUGCUCUUUUCUAUAUAU 18 downstream (SEQ ID NO: 2335) CEP290-1527 + GAACAAGUUUUGAAACAGGAA 21 downstream (SEQ ID NO: 2336) CEP290-1528 + GUAAUGCCUGAACAAGUUUUGAAA 24 downstream (SEQ ID NO: 2337) CEP290-1529 + GCCUGAACAAGUUUUGAAA 19 downstream (SEQ ID NO: 2338) CEP290-1530 + GGUAAUGCCUGAACAAGUU 19 downstream (SEQ ID NO: 2339) CEP290-1531 + GUAAUGCCUGAACAAGUU 18 downstream (SEQ ID NO: 2340) CEP290-1532 - GUACGUGCUCUUUUCUAUAUA 21 downstream (SEQ ID NO: 2341) CEP290-1533 + GAGAGAAAUGGUUCCCUAUAUA 22 downstream (SEQ ID NO: 2342) CEP290-1534 + GAGAAAUGGUUCCCUAUAUA 20 downstream (SEQ ID NO: 771) CEP290-1535 + GAAAUGGUUCCCUAUAUA 18 downstream (SEQ ID NO: 2344) CEP290-1536 - GCUUAGGAAAUUAUUGUUGCUUU 23 downstream (SEQ ID NO: 2345) CEP290-1537 - GGAAAUUAUUGUUGCUUU 18 downstream (SEQ ID NO: 2346) CEP290-1538 - GCUUUUUGAGAGGUAAAGGUUC 22 downstream (SEQ ID NO: 2347) CEP290-1539 + GAGCAAAACAACUGGAAGA 19 downstream (SEQ ID NO: 2348) CEP290-1540 - GUGUGAAGAAUGGAAUAGAUAAU 23 downstream (SEQ ID NO: 2349) CEP290-1541 - GUGAAGAAUGGAAUAGAUAAU 21 downstream (SEQ ID NO: 2350) CEP290-1542 - GAAGAAUGGAAUAGAUAAU 19 downstream (SEQ ID NO: 2351) CEP290-1543 + GUAAGGAGGAUGUAAGACUGGAGA 24 downstream (SEQ ID NO: 2352) CEP290-1544 + GGAGGAUGUAAGACUGGAGA 20 downstream (SEQ ID NO: 779) CEP290-1545 + GAGGAUGUAAGACUGGAGA 19 downstream (SEQ ID NO: 2354) CEP290-1546 - GAAAAACUUGAAAUUUGAUAGUAG 24 downstream (SEQ ID NO: 2355) CEP290-1547 - GUGUUUACAUAUCUGUCUUCCUUA 24 downstream (SEQ ID NO: 2356) CEP290-1548 - GUUUACAUAUCUGUCUUCCUUA 22 downstream (SEQ ID NO: 2357) CEP290-1549 + GUUCCAUUAAAAAAAGUAUGCUU 23 downstream (SEQ ID NO: 2358) CEP290-1550 - GGAAUAUAAGUCUUUUGAUAU 21 downstream (SEQ ID NO: 2359) CEP290-1551 - GAAUAUAAGUCUUUUGAUAU 20 downstream (SEQ ID NO: 770) CEP290-1552 - GUGUGAAGAAUGGAAUAGAUAAUA 24 downstream (SEQ ID NO: 2361) CEP290-1553 - GUGAAGAAUGGAAUAGAUAAUA 22 downstream (SEQ ID NO: 2362) CEP290-1554 - GAAGAAUGGAAUAGAUAAUA 20 downstream (SEQ ID NO: 467) CEP290-1555 - GGAUGGGUAAUAAAGCAA 18 downstream (SEQ ID NO: 2363) CEP290-1556 + GAAAUUCACUGAGCAAAACAA 21 downstream (SEQ ID NO: 2364) CEP290-1557 + GGAUGUAAGACUGGAGAUAGAGA 23 downstream (SEQ ID NO: 2365) CEP290-1558 + GAUGUAAGACUGGAGAUAGAGA 22 downstream (SEQ ID NO: 2366) CEP290-1559 + GUAAGACUGGAGAUAGAGA 19 downstream (SEQ ID NO: 2367) CEP290-1560 - GAAAUUUGAUAGUAGAAGAAAA 22 downstream (SEQ ID NO: 2368) CEP290-1561 - GGGUAAUAAAGCAAAAGAAAAAC 23 downstream (SEQ ID NO: 2369) CEP290-1562 - GGUAAUAAAGCAAAAGAAAAAC 22 downstream (SEQ ID NO: 2370) CEP290-1563 - GUAAUAAAGCAAAAGAAAAAC 21 downstream (SEQ ID NO: 2371) CEP290-1564 + GCACUCCAGCCUGGGCAACACA 22 downstream (SEQ ID NO: 2372) CEP290-1565 - UACUUACCUCAUGUCAUCUAGAGC 24 downstream (SEQ ID NO: 2373) CEP290-1566 - UUACCUCAUGUCAUCUAGAGC 21 downstream (SEQ ID NO: 2374) CEP290-1567 - UACCUCAUGUCAUCUAGAGC 20 downstream (SEQ ID NO: 876) CEP290-1568 + UUUUUAAGGCGGGGAGUCAC 20 downstream (SEQ ID NO: 909) CEP290-1569 + UUUUAAGGCGGGGAGUCAC 19 downstream (SEQ ID NO: 2377) CEP290-1570 + UUUAAGGCGGGGAGUCAC 18 downstream (SEQ ID NO: 2378) CEP290-1571 - UUGGCACAGAGUUCAAGCUAAUAC 24 downstream (SEQ ID NO: 2379) CEP290-1572 - UGGCACAGAGUUCAAGCUAAUAC 23 downstream (SEQ ID NO: 2380) CEP290-1573 + UUAGCUUGAACUCUGUGCCAAAC 23 downstream (SEQ ID NO: 2381) CEP290-1574 + UAGCUUGAACUCUGUGCCAAAC 22 downstream (SEQ ID NO: 2382) CEP290-1575 + UUGAACUCUGUGCCAAAC 18 downstream (SEQ ID NO: 2383) CEP290-1576 - UGUGGUGUCAAAUAUGGUGCU 21 downstream (SEQ ID NO: 2384) CEP290-1577 - UGGUGUCAAAUAUGGUGCU 19 downstream (SEQ ID NO: 2385) CEP290-1578 - UGUGGUGUCAAAUAUGGUGCUU 22 downstream (SEQ ID NO: 2386) CEP290-1579 - UGGUGUCAAAUAUGGUGCUU 20 downstream (SEQ ID NO: 625) CEP290-1580 + UGCUCUAGAUGACAUGAGGUAAGU 24 downstream (SEQ ID NO: 2388) CEP290-1581 + UCUAGAUGACAUGAGGUAAGU 21 downstream (SEQ ID NO: 2389) CEP290-1582 + UAGAUGACAUGAGGUAAGU 19 downstream (SEQ ID NO: 2390) CEP290-1583 - UAAUACAUGAGAGUGAUUAGUGG 23 downstream (SEQ ID NO: 2391) CEP290-1584 - UACAUGAGAGUGAUUAGUGG 20 downstream (SEQ ID NO: 628) CEP290-1585 - UAAAGGUUCAUGAGACUAGAGGUC 24 downstream (SEQ ID NO: 2392) CEP290-1586 - UUCAUGAGACUAGAGGUC 18 downstream (SEQ ID NO: 2393) CEP290-1587 + UGGCAGUAAGGAGGAUGUAAGAC 23 downstream (SEQ ID NO: 2394) CEP290-1588 + UAGCUUUUGACAGUUUUUAAGG 22 downstream (SEQ ID NO: 2395) CEP290-1589 + UUUUGACAGUUUUUAAGG 18 downstream (SEQ ID NO: 2396) CEP290-1590 - UUGUACGUGCUCUUUUCUAUAUAU 24 downstream (SEQ ID NO: 2397) CEP290-1591 - UGUACGUGCUCUUUUCUAUAUAU 23 downstream (SEQ ID NO: 2398) CEP290-1592 - UACGUGCUCUUUUCUAUAUAU 21 downstream (SEQ ID NO: 2399) CEP290-1593 + UUCACUGAGCAAAACAACUGG 21 downstream (SEQ ID NO: 2400) CEP290-1594 + UCACUGAGCAAAACAACUGG 20 downstream (SEQ ID NO: 883) CEP290-1595 + UGAACAAGUUUUGAAACAGGAA 22 downstream (SEQ ID NO: 2402) CEP290-1596 + UAAUGCCUGAACAAGUUUUGAAA 23 downstream (SEQ ID NO: 2403) CEP290-1597 + UGCCUGAACAAGUUUUGAAA 20 downstream (SEQ ID NO: 897) CEP290-1598 + UUCACUGAGCAAAACAACUGGAA 23 downstream (SEQ ID NO: 2405) CEP290-1599 + UCACUGAGCAAAACAACUGGAA 22 downstream (SEQ ID NO: 2406) CEP290-1600 + UGAGCAAAACAACUGGAA 18 downstream (SEQ ID NO: 2407) CEP290-1601 - UUUGUACGUGCUCUUUUCUAUAUA 24 downstream (SEQ ID NO: 2408) CEP290-1602 - UUGUACGUGCUCUUUUCUAUAUA 23 downstream (SEQ ID NO: 2409) CEP290-1603 - UGUACGUGCUCUUUUCUAUAUA 22 downstream (SEQ ID NO: 2410) CEP290-1604 - UACGUGCUCUUUUCUAUAUA 20 downstream (SEQ ID NO: 877) CEP290-1605 + UAUUAUCUAUUCCAUUCUUCACAC 24 downstream (SEQ ID NO: 2412) CEP290-1606 + UUAUCUAUUCCAUUCUUCACAC 22 downstream (SEQ ID NO: 2413) CEP290-1607 + UAUCUAUUCCAUUCUUCACAC 21 downstream (SEQ ID NO: 2414) CEP290-1608 + UCUAUUCCAUUCUUCACAC 19 downstream (SEQ ID NO: 2415) CEP290-1609 - UGCUUAGGAAAUUAUUGUUGCUUU 24 downstream (SEQ ID NO: 2416) CEP290-1610 - UUAGGAAAUUAUUGUUGCUUU 21 downstream (SEQ ID NO: 2417) CEP290-1611 - UAGGAAAUUAUUGUUGCUUU 20 downstream (SEQ ID NO: 2418) CEP290-1612 - UUGCUUUUUGAGAGGUAAAGGUUC 24 downstream (SEQ ID NO: 2419) CEP290-1613 - UGCUUUUUGAGAGGUAAAGGUUC 23 downstream (SEQ ID NO: 2420) CEP290-1614 - UUUUUGAGAGGUAAAGGUUC 20 downstream (SEQ ID NO: 2421) CEP290-1615 - UUUUGAGAGGUAAAGGUUC 19 downstream (SEQ ID NO: 2422) CEP290-1616 - UUUGAGAGGUAAAGGUUC 18 downstream (SEQ ID NO: 2423) CEP290-1617 + UCACUGAGCAAAACAACUGGAAGA 24 downstream (SEQ ID NO: 2424) CEP290-1618 + UGAGCAAAACAACUGGAAGA 20 downstream (SEQ ID NO: 894) CEP290-1619 + UACAUAAGAAAGAACACUGUGGU 23 downstream (SEQ ID NO: 2426) CEP290-1620 + UAAGAAAGAACACUGUGGU 19 downstream (SEQ ID NO: 2427) CEP290-1621 - UGUGUGAAGAAUGGAAUAGAUAAU 24 downstream (SEQ ID NO: 2428) CEP290-1622 - UGUGAAGAAUGGAAUAGAUAAU 22 downstream (SEQ ID NO: 2429) CEP290-1623 - UGAAGAAUGGAAUAGAUAAU 20 downstream (SEQ ID NO: 2430) CEP290-1624 + UAAGGAGGAUGUAAGACUGGAGA 23 downstream (SEQ ID NO: 2431) CEP290-1625 - UGUUUACAUAUCUGUCUUCCUUA 23 downstream (SEQ ID NO: 2432) CEP290-1626 - UUUACAUAUCUGUCUUCCUUA 21 downstream (SEQ ID NO: 2433) CEP290-1627 - UUACAUAUCUGUCUUCCUUA 20 downstream (SEQ ID NO: 901) CEP290-1628 - UACAUAUCUGUCUUCCUUA 19 downstream (SEQ ID NO: 2435) CEP290-1629 + UGUUCCAUUAAAAAAAGUAUGCUU 24 downstream (SEQ ID NO: 2436) CEP290-1630 + UUCCAUUAAAAAAAGUAUGCUU 22 downstream (SEQ ID NO: 2437) CEP290-1631 + UCCAUUAAAAAAAGUAUGCUU 21 downstream (SEQ ID NO: 2438) CEP290-1632 + UAUCAAAAGACUUAUAUUCCAUU 23 downstream (SEQ ID NO: 2439) CEP290-1633 + UCAAAAGACUUAUAUUCCAUU 21 downstream (SEQ ID NO: 2440) CEP290-1634 - UCAGAUUUCAUGUGUGAAGA 20 downstream (SEQ ID NO: 2441) CEP290-1635 - UGGAAUAUAAGUCUUUUGAUAU 22 downstream (SEQ ID NO: 2442) CEP290-1636 - UGUGAAGAAUGGAAUAGAUAAUA 23 downstream (SEQ ID NO: 2443) CEP290-1637 - UGAAGAAUGGAAUAGAUAAUA 21 downstream (SEQ ID NO: 2444) CEP290-1638 - UGGAUGGGUAAUAAAGCAA 19 downstream (SEQ ID NO: 2445) CEP290-1639 + UAGAAAUUCACUGAGCAAAACAA 23 downstream (SEQ ID NO: 2446) CEP290-1640 + UGUAAGACUGGAGAUAGAGA 20 downstream (SEQ ID NO: 898) CEP290-1641 + UAAGACUGGAGAUAGAGA 18 downstream (SEQ ID NO: 2448) CEP290-1642 - UUGAAAUUUGAUAGUAGAAGAAAA 24 downstream (SEQ ID NO: 2449) CEP290-1643 - UGAAAUUUGAUAGUAGAAGAAAA 23 downstream (SEQ ID NO: 2450) CEP290-1644 - UUUGAUAGUAGAAGAAAA 18 downstream (SEQ ID NO: 2451) CEP290-1645 + UAAAACUAAGACACUGCCAA 20 downstream (SEQ ID NO: 871) CEP290-1646 - UUUUUCUUAAGCAUACUUUUUUUA 24 downstream (SEQ ID NO: 2453) CEP290-1647 - UUUUCUUAAGCAUACUUUUUUUA 23 downstream (SEQ ID NO: 2454) CEP290-1648 - UUUCUUAAGCAUACUUUUUUUA 22 downstream (SEQ ID NO: 2455) CEP290-1649 - UUCUUAAGCAUACUUUUUUUA 21 downstream (SEQ ID NO: 2456) CEP290-1650 - UCUUAAGCAUACUUUUUUUA 20 downstream (SEQ ID NO: 891) CEP290-1651 - UUAAGCAUACUUUUUUUA 18 downstream (SEQ ID NO: 2458) CEP290-1652 - UGGGUAAUAAAGCAAAAGAAAAAC 24 downstream (SEQ ID NO: 2459) CEP290-1653 - UAAUAAAGCAAAAGAAAAAC 20 downstream (SEQ ID NO: 2460) CEP290-1654 - UUCUUUUUUUGUUGUUUUUUUUU 23 downstream (SEQ ID NO: 2461) CEP290-1655 - UCUUUUUUUGUUGUUUUUUUUU 22 downstream (SEQ ID NO: 2462) CEP290-1656 - UUUUUUUGUUGUUUUUUUUU 20 downstream (SEQ ID NO: 2463) CEP290-1657 - UUUUUUGUUGUUUUUUUUU 19 downstream (SEQ ID NO: 2464) CEP290-1658 - UUUUUGUUGUUUUUUUUU 18 downstream (SEQ ID NO: 2465) CEP290-1659 + UGCACUCCAGCCUGGGCAACACA 23 downstream (SEQ ID NO: 2466) CEP290-1660 + UCCAGCCUGGGCAACACA 18 downstream (SEQ ID NO: 2467) CEP290-1661 + AUUUUCGUGACCUCUAGUCUC 21 downstream (SEQ ID NO: 2468) CEP290-1662 + ACUAAUCACUCUCAUGUAUUAGC 23 downstream (SEQ ID NO: 2469) CEP290-1663 + AAUCACUCUCAUGUAUUAGC 20 downstream (SEQ ID NO: 814) CEP290-1664 + AUCACUCUCAUGUAUUAGC 19 downstream (SEQ ID NO: 2471) CEP290-1665 + AGAUGACAUGAGGUAAGUA 19 downstream (SEQ ID NO: 2472) CEP290-1666 - ACCUCAUGUCAUCUAGAGCAAGAG 24 downstream (SEQ ID NO: 2473) CEP290-1667 - AUGUCAUCUAGAGCAAGAG 19 downstream (SEQ ID NO: 2474) CEP290-1668 - AAUACAUGAGAGUGAUUAGUGGUG 24 downstream (SEQ ID NO: 2475) CEP290-1669 - AUACAUGAGAGUGAUUAGUGGUG 23 downstream (SEQ ID NO: 2476) CEP290-1670 - ACAUGAGAGUGAUUAGUGGUG 21 downstream (SEQ ID NO: 2477) CEP290-1671 - AUGAGAGUGAUUAGUGGUG 19 downstream (SEQ ID NO: 2478) CEP290-1672 - ACGUGCUCUUUUCUAUAUAUA 21 downstream (SEQ ID NO: 2479) CEP290-1673 + ACAAAACCUAUGUAUAAGAUG 21 downstream (SEQ ID NO: 2480) CEP290-1674 + AAAACCUAUGUAUAAGAUG 19 downstream (SEQ ID NO: 2481) CEP290-1675 + AAACCUAUGUAUAAGAUG 18 downstream (SEQ ID NO: 2482) CEP290-1676 + AUAUAUAGAAAAGAGCACGUACAA 24 downstream (SEQ ID NO: 2483) CEP290-1677 + AUAUAGAAAAGAGCACGUACAA 22 downstream (SEQ ID NO: 2484) CEP290-1678 + AUAGAAAAGAGCACGUACAA 20 downstream (SEQ ID NO: 832) CEP290-1679 + AGAAAAGAGCACGUACAA 18 downstream (SEQ ID NO: 2486) CEP290-1680 + AGAAAUGGUUCCCUAUAUAUAGAA 24 downstream (SEQ ID NO: 2487) CEP290-1681 + AAAUGGUUCCCUAUAUAUAGAA 22 downstream (SEQ ID NO: 2488) CEP290-1682 + AAUGGUUCCCUAUAUAUAGAA 21 downstream (SEQ ID NO: 2489) CEP290-1683 + AUGGUUCCCUAUAUAUAGAA 20 downstream (SEQ ID NO: 839) CEP290-1684 - AUGGAAUAUAAGUCUUUUGAUAUA 24 downstream (SEQ ID NO: 2491) CEP290-1685 - AAUAUAAGUCUUUUGAUAUA 20 downstream (SEQ ID NO: 687) CEP290-1686 - AUAUAAGUCUUUUGAUAUA 19 downstream (SEQ ID NO: 2493) CEP290-1687 + ACGUACAAAAGAACAUACAUAAGA 24 downstream (SEQ ID NO: 2494) CEP290-1688 + ACAAAAGAACAUACAUAAGA 20 downstream (SEQ ID NO: 816) CEP290-1689 + AAAAGAACAUACAUAAGA 18 downstream (SEQ ID NO: 2496) CEP290-1690 + AAGAAAAAAAAGGUAAUGC 19 downstream (SEQ ID NO: 2497) CEP290-1691 + AGAAAAAAAAGGUAAUGC 18 downstream (SEQ ID NO: 2498) CEP290-1692 + AAACAGGAAUAGAAAUUCA 19 downstream (SEQ ID NO: 2499) CEP290-1693 + AACAGGAAUAGAAAUUCA 18 downstream (SEQ ID NO: 2500) CEP290-1694 + AAGAUCACUCCACUGCACUCCAGC 24 downstream (SEQ ID NO: 2501) CEP290-1695 + AGAUCACUCCACUGCACUCCAGC 23 downstream (SEQ ID NO: 2502) CEP290-1696 + AUCACUCCACUGCACUCCAGC 21 downstream (SEQ ID NO: 2503) CEP290-1697 + ACUCCACUGCACUCCAGC 18 downstream (SEQ ID NO: 2504) CEP290-1698 - CCCCUACUUACCUCAUGUCAUC 22 downstream (SEQ ID NO: 2505) CEP290-1699 - CCCUACUUACCUCAUGUCAUC 21 downstream (SEQ ID NO: 2506) CEP290-1700 - CCUACUUACCUCAUGUCAUC 20 downstream (SEQ ID NO: 747) CEP290-1701 - CUACUUACCUCAUGUCAUC 19 downstream (SEQ ID NO: 2508) CEP290-1702 + CUGAUUUUCGUGACCUCUAGUCUC 24 downstream (SEQ ID NO: 2509) CEP290-1703 + CACUAAUCACUCUCAUGUAUUAGC 24 downstream (SEQ ID NO: 2510) CEP290-1704 + CUAAUCACUCUCAUGUAUUAGC 22 downstream (SEQ ID NO: 2511) CEP290-1705 + CUCUAGAUGACAUGAGGUAAGUA 23 downstream (SEQ ID NO: 2512) CEP290-1706 + CUAGAUGACAUGAGGUAAGUA 21 downstream (SEQ ID NO: 2513) CEP290-1707 - CCUCAUGUCAUCUAGAGCAAGAG 23 downstream (SEQ ID NO: 2514) CEP290-1708 - CUCAUGUCAUCUAGAGCAAGAG 22 downstream (SEQ ID NO: 2515) CEP290-1709 - CAUGUCAUCUAGAGCAAGAG 20 downstream (SEQ ID NO: 855) CEP290-1710 - CAUGAGAGUGAUUAGUGGUG 20 downstream (SEQ ID NO: 854) CEP290-1711 - CGUGCUCUUUUCUAUAUAUA 20 downstream (SEQ ID NO: 624) CEP290-1712 + CAAAACCUAUGUAUAAGAUG 20 downstream (SEQ ID NO: 841) CEP290-1713 + CGUACAAAAGAACAUACAUAAGA 23 downstream (SEQ ID NO: 2520) CEP290-1714 + CAAAAGAACAUACAUAAGA 19 downstream (SEQ ID NO: 2521) CEP290-1715 + CUUAAGAAAAAAAAGGUAAUGC 22 downstream (SEQ ID NO: 2522) CEP290-1716 - CUUAAGCAUACUUUUUUUAA 20 downstream (SEQ ID NO: 690) CEP290-1717 + CACUCCACUGCACUCCAGC 19 downstream (SEQ ID NO: 2524) CEP290-132 - GUCCCCUACUUACCUCAUGUCAUC 24 downstream (SEQ ID NO: 2525) CEP290-1718 + GAUUUUCGUGACCUCUAGUCUC 22 downstream (SEQ ID NO: 2526) CEP290-1719 + GCUCUAGAUGACAUGAGGUAAGUA 24 downstream (SEQ ID NO: 2527) CEP290-1720 + GAUGACAUGAGGUAAGUA 18 downstream (SEQ ID NO: 2528) CEP290-1721 - GUACGUGCUCUUUUCUAUAUAUA 23 downstream (SEQ ID NO: 2529) CEP290-1722 - GUGCUCUUUUCUAUAUAUA 19 downstream (SEQ ID NO: 2530) CEP290-1723 + GUACAAAACCUAUGUAUAAGAUG 23 downstream (SEQ ID NO: 2531) CEP290-1724 + GAAAUGGUUCCCUAUAUAUAGAA 23 downstream (SEQ ID NO: 2532) CEP290-1725 + GGUUCCCUAUAUAUAGAA 18 downstream (SEQ ID NO: 2533) CEP290-1726 - GGAAUAUAAGUCUUUUGAUAUA 22 downstream (SEQ ID NO: 2534) CEP290-1727 - GAAUAUAAGUCUUUUGAUAUA 21 downstream (SEQ ID NO: 2535) CEP290-1728 + GUACAAAAGAACAUACAUAAGA 22 downstream (SEQ ID NO: 2536) CEP290-1729 + GCUUAAGAAAAAAAAGGUAAUGC 23 downstream (SEQ ID NO: 2537) CEP290-1730 + GAAACAGGAAUAGAAAUUCA 20 downstream (SEQ ID NO: 769) CEP290-1731 + GAUCACUCCACUGCACUCCAGC 22 downstream (SEQ ID NO: 2539) CEP290-1732 - UCCCCUACUUACCUCAUGUCAUC 23 downstream (SEQ ID NO: 2540) CEP290-1733 - UACUUACCUCAUGUCAUC 18 downstream (SEQ ID NO: 2541) CEP290-1734 + UGAUUUUCGUGACCUCUAGUCUC 23 downstream (SEQ ID NO: 2542) CEP290-1735 + UUUUCGUGACCUCUAGUCUC 20 downstream (SEQ ID NO: 2543) CEP290-1736 + UUUCGUGACCUCUAGUCUC 19 downstream (SEQ ID NO: 2544) CEP290-1737 + UUCGUGACCUCUAGUCUC 18 downstream (SEQ ID NO: 2545) CEP290-1738 + UAAUCACUCUCAUGUAUUAGC 21 downstream (SEQ ID NO: 2546) CEP290-1739 + UCACUCUCAUGUAUUAGC 18 downstream (SEQ ID NO: 2547) CEP290-1740 + UCUAGAUGACAUGAGGUAAGUA 22 downstream (SEQ ID NO: 2548) CEP290-1741 + UAGAUGACAUGAGGUAAGUA 20 downstream (SEQ ID NO: 680) CEP290-1742 - UCAUGUCAUCUAGAGCAAGAG 21 downstream (SEQ ID NO: 2550) CEP290-1743 - UGUCAUCUAGAGCAAGAG 18 downstream (SEQ ID NO: 2551) CEP290-1744 - UACAUGAGAGUGAUUAGUGGUG 22 downstream (SEQ ID NO: 2552) CEP290-1745 - UGAGAGUGAUUAGUGGUG 18 downstream (SEQ ID NO: 2553) CEP290-1746 - UGUACGUGCUCUUUUCUAUAUAUA 24 downstream (SEQ ID NO: 2554) CEP290-1747 - UACGUGCUCUULUCUAUAUAUA 22 downstream (SEQ ID NO: 2555) CEP290-1748 - UGCUCUUUUCUAUAUAUA 18 downstream (SEQ ID NO: 2556) CEP290-1749 + UGUACAAAACCUAUGUAUAAGAUG 24 downstream (SEQ ID NO: 2557) CEP290-1750 + UACAAAACCUAUGUAUAAGAUG 22 downstream (SEQ ID NO: 2558) CEP290-1751 + UAUAUAGAAAAGAGCACGUACAA 23 downstream (SEQ ID NO: 2559) CEP290-1752 + UAUAGAAAAGAGCACGUACAA 21 downstream (SEQ ID NO: 2560) CEP290-1753 + UAGAAAAGAGCACGUACAA 19 downstream (SEQ ID NO: 2561) CEP290-1754 + UGGUUCCCUAUAUAUAGAA 19 downstream (SEQ ID NO: 2562) CEP290-1755 - UGGAAUAUAAGUCUUUUGAUAUA 23 downstream (SEQ ID NO: 2563) CEP290-1756 - UAUAAGUCUUUUGAUAUA 18 downstream (SEQ ID NO: 2564) CEP290-1757 + UACAAAAGAACAUACAUAAGA 21 downstream (SEQ ID NO: 2565) CEP290-1758 + UGCUUAAGAAAAAAAAGGUAAUGC 24 downstream (SEQ ID NO: 2566) CEP290-1759 + UUAAGAAAAAAAAGGUAAUGC 21 downstream (SEQ ID NO: 2567) CEP290-1760 + UAAGAAAAAAAAGGUAAUGC 20 downstream (SEQ ID NO: 872) CEP290-1761 + UUUUGAAACAGGAAUAGAAAUUCA 24 downstream (SEQ ID NO: 2569) CEP290-1762 + UUUGAAACAGGAAUAGAAAUUCA 23 downstream (SEQ ID NO: 2570) CEP290-1763 + UUGAAACAGGAAUAGAAAUUCA 22 downstream (SEQ ID NO: 2571) CEP290-1764 + UGAAACAGGAAUAGAAAUUCA 21 downstream (SEQ ID NO: 2572) CEP290-1765 - UUUUCUUAAGCAUACUUUUUUUAA 24 downstream (SEQ ID NO: 2573) CEP290-1766 - UUUCUUAAGCAUACUUUUUUUAA 23 downstream (SEQ ID NO: 2574) CEP290-1767 - UUCUUAAGCAUACUUUUUUUAA 22 downstream (SEQ ID NO: 2575) CEP290-1768 - UCUUAAGCAUACUUUUUUUAA 21 downstream (SEQ ID NO: 2576) CEP290-1769 - UUAAGCAUACUUUUUUUAA 19 downstream (SEQ ID NO: 2577) CEP290-1770 - UAAGCAUACUUUUUUUAA 18 downstream (SEQ ID NO: 2578) CEP290-1771 + UCACUCCACUGCACUCCAGC 20 downstream (SEQ ID NO: 2579) CEP290-1772 + AGUUUUUAAGGCGGGGAGUCACA 23 downstream (SEQ ID NO: 2580) CEP290-1773 - AAACUGUCAAAAGCUACCGGUUAC 24 downstream (SEQ ID NO: 2581) CEP290-1774 - AACUGUCAAAAGCUACCGGUUAC 23 downstream (SEQ ID NO: 2582) CEP290-252 + ACUGUCAAAAGCUACCGGUUAC 22 downstream (SEQ ID NO: 2583) CEP290-1775 + AGUUCAUCUCUUGCUCUAGAUGAC 24 downstream (SEQ ID NO: 2584) CEP290-1776 + AUCUCUUGCUCUAGAUGAC 19 downstream (SEQ ID NO: 2585) CEP290-1777 - ACGAAAAUCAGAUUUCAUGU 20 downstream (SEQ ID NO: 2586) CEP290-1778 - AAUACAUGAGAGUGAUUAGUG 21 downstream (SEQ ID NO: 2587) CEP290-1779 - AUACAUGAGAGUGAUUAGUG 20 downstream (SEQ ID NO: 831) CEP290-1780 - ACAUGAGAGUGAUUAGUG 18 downstream (SEQ ID NO: 2589) CEP290-1781 + AUUAGCUUGAACUCUGUGCCAAA 23 downstream (SEQ ID NO: 2590) CEP290-1782 + AGCUUGAACUCUGUGCCAAA 20 downstream (SEQ ID NO: 824) CEP290-1783 - AUGUAGAUUGAGGUAGAAUCAAG 23 downstream (SEQ ID NO: 2592) CEP290-1784 - AGAUUGAGGUAGAAUCAAG 19 downstream (SEQ ID NO: 2593) CEP290-1785 + AUAAGAUGCAGAACUAGUGUAGA 23 downstream (SEQ ID NO: 2594) CEP290-1786 + AAGAUGCAGAACUAGUGUAGA 21 downstream (SEQ ID NO: 2595) CEP290-1787 + AGAUGCAGAACUAGUGUAGA 20 downstream (SEQ ID NO: 821) CEP290-1788 + AUGCAGAACUAGUGUAGA 18 downstream (SEQ ID NO: 2597) CEP290-1789 - AUAGAUGUAGAUUGAGGUAGAAUC 24 downstream (SEQ ID NO: 2598) CEP290-1790 - AGAUGUAGAUUGAGGUAGAAUC 22 downstream (SEQ ID NO: 2599) CEP290-1791 - AUGUAGAUUGAGGUAGAAUC 20 downstream (SEQ ID NO: 2600) CEP290-1792 + AGAAUGAUCAUUCUUGUGGCAGUA 24 downstream (SEQ ID NO: 2601) CEP290-1793 + AAUGAUCAUUCUUGUGGCAGUA 22 downstream (SEQ ID NO: 2602) CEP290-1794 + AUGAUCAUUCUUGUGGCAGUA 21 downstream (SEQ ID NO: 2603) CEP290-1795 + AUCAUUCUUGUGGCAGUA 18 downstream (SEQ ID NO: 2604) CEP290-1796 + AGAAUGAUCAUUCUUGUGGCAGU 23 downstream (SEQ ID NO: 2605) CEP290-1797 + AAUGAUCAUUCUUGUGGCAGU 21 downstream (SEQ ID NO: 2606) CEP290-1798 + AUGAUCAUUCUUGUGGCAGU 20 downstream (SEQ ID NO: 837) CEP290-1799 - AGAGGUAAAGGUUCAUGAGAC 21 downstream (SEQ ID NO: 2608) CEP290-1800 - AGGUAAAGGUUCAUGAGAC 19 downstream (SEQ ID NO: 2609) CEP290-1801 + AGCUUUUGACAGUUUUUAAG 20 downstream (SEQ ID NO: 825) CEP290-1802 + AGCUUUUGACAGUUUUUAAGGC 22 downstream (SEQ ID NO: 2611) CEP290-1803 + AGAAAUUCACUGAGCAAAACAAC 23 downstream (SEQ ID NO: 2612) CEP290-1804 + AAAUUCACUGAGCAAAACAAC 21 downstream (SEQ ID NO: 2613) CEP290-1805 + AAUUCACUGAGCAAAACAAC 20 downstream (SEQ ID NO: 678) CEP290-1806 + AUUCACUGAGCAAAACAAC 19 downstream (SEQ ID NO: 2615) CEP290-1807 + AGUAAGGAGGAUGUAAGA 18 downstream (SEQ ID NO: 2616) CEP290-1808 + AUCAAAAGACUUAUAUUCCAUUA 23 downstream (SEQ ID NO: 2617) CEP290-1809 + AAAAGACUUAUAUUCCAUUA 20 downstream (SEQ ID NO: 685) CEP290-1810 + AAAGACUUAUAUUCCAUUA 19 downstream (SEQ ID NO: 2619) CEP290-1811 + AAGACUUAUAUUCCAUUA 18 downstream (SEQ ID NO: 2620) CEP290-1812 - AGGAAAUUAUUGUUGCUUUUU 21 downstream (SEQ ID NO: 2621) CEP290-1813 - AAAUUAUUGUUGCUUUUU 18 downstream (SEQ ID NO: 2622) CEP290-1814 - AAAGAAAAACUUGAAAUUUGAUAG 24 downstream (SEQ ID NO: 2623) CEP290-1815 - AAGAAAAACUUGAAAUUUGAUAG 23 downstream (SEQ ID NO: 2624) CEP290-1816 - AGAAAAACUUGAAAUUUGAUAG 22 downstream (SEQ ID NO: 2625) CEP290-1817 - AAAAACUUGAAAUUUGAUAG 20 downstream (SEQ ID NO: 2626) CEP290-1818 - AAAACUUGAAAUUUGAUAG 19 downstream (SEQ ID NO: 2627) CEP290-1819 - AAACUUGAAAUUUGAUAG 18 downstream (SEQ ID NO: 2628) CEP290-1820 - AAGAAAAAAGAAAUAGAUGUAGA 23 downstream (SEQ ID NO: 2629) CEP290-1821 - AGAAAAAAGAAAUAGAUGUAGA 22 downstream (SEQ ID NO: 2630) CEP290-1822 - AAAAAAGAAAUAGAUGUAGA 20 downstream (SEQ ID NO: 2631) CEP290-1823 - AAAAAGAAAUAGAUGUAGA 19 downstream (SEQ ID NO: 2632) CEP290-1824 - AAAAGAAAUAGAUGUAGA 18 downstream (SEQ ID NO: 2633) CEP290-1825 - AGAGUCUCACUGUGUUGCCCAGG 23 downstream (SEQ ID NO: 2634) CEP290-1826 - AGUCUCACUGUGUUGCCCAGG 21 downstream (SEQ ID NO: 2635) CEP290-1827 + CAGUUUUUAAGGCGGGGAGUCACA 24 downstream (SEQ ID NO: 2636) CEP290-1828 - CUGUCAAAAGCUACCGGUUAC 21 downstream (SEQ ID NO: 2637) CEP290-1829 + CAUCUCUUGCUCUAGAUGAC 20 downstream (SEQ ID NO: 853) CEP290-1830 - CACGAAAAUCAGAUUUCAUGU 21 downstream (SEQ ID NO: 2639) CEP290-1831 - CGAAAAUCAGAUUUCAUGU 19 downstream (SEQ ID NO: 2640) CEP290-1832 - CUAAUACAUGAGAGUGAUUAGUG 23 downstream (SEQ ID NO: 2641) CEP290-1833 + CUUGAACUCUGUGCCAAA 18 downstream (SEQ ID NO: 2642) CEP290-1834 + CUCUAGAUGACAUGAGGUAAG 21 downstream (SEQ ID NO: 2643) CEP290-1835 + CUAGAUGACAUGAGGUAAG 19 downstream (SEQ ID NO: 2644) CEP290-1836 + CGGUAGCUUUUGACAGUUUUUAAG 24 downstream (SEQ ID NO: 2645) CEP290-1837 + CUUUUGACAGUUUUUAAG 18 downstream (SEQ ID NO: 2646) CEP290-1838 + CUUUUGACAGUUUUUAAGGC 20 downstream (SEQ ID NO: 684) CEP290-1839 + CAGUAAGGAGGAUGUAAGA 19 downstream (SEQ ID NO: 2648) CEP290-1840 + CAAAAGACUUAUAUUCCAUUA 21 downstream (SEQ ID NO: 2649) CEP290-1841 - CUUAGGAAAUUAUUGUUGCUUUUU 24 downstream (SEQ ID NO: 2650) CEP290-1842 - CUGUGUUGCCCAGGCUGGAGUGCA 24 downstream (SEQ ID NO: 2651) CEP290-1843 - CAGAGUCUCACUGUGUUGCCCAGG 24 downstream (SEQ ID NO: 2652) CEP290-1844 - CUCACUGUGUUGCCCAGG 18 downstream (SEQ ID NO: 2653) CEP290-1845 + GUUUUUAAGGCGGGGAGUCACA 22 downstream (SEQ ID NO: 2654) CEP290-1846 - GUCAAAAGCUACCGGUUAC 19 downstream (SEQ ID NO: 2655) CEP290-1847 + GUUCAUCUCUUGCUCUAGAUGAC 23 downstream (SEQ ID NO: 2656) CEP290-1848 - GGUCACGAAAAUCAGAUUUCAUGU 24 downstream (SEQ ID NO: 2657) CEP290-1849 - GUCACGAAAAUCAGAUUUCAUGU 23 downstream (SEQ ID NO: 2658) CEP290-1850 - GAAAAUCAGAUUUCAUGU 18 downstream (SEQ ID NO: 2659) CEP290-1851 - GCUAAUACAUGAGAGUGAUUAGUG 24 downstream (SEQ ID NO: 2660) CEP290-1852 + GCUUGAACUCUGUGCCAAA 19 downstream (SEQ ID NO: 2661) CEP290-1853 + GCUCUAGAUGACAUGAGGUAAG 22 downstream (SEQ ID NO: 2662) CEP290-1854 - GAUGUAGAUUGAGGUAGAAUCAAG 24 downstream (SEQ ID NO: 2663) CEP290-1855 - GUAGAUUGAGGUAGAAUCAAG 21 downstream (SEQ ID NO: 2664) CEP290-1856 - GAUUGAGGUAGAAUCAAG 18 downstream (SEQ ID NO: 2665) CEP290-1857 + GAUGCAGAACUAGUGUAGA 19 downstream (SEQ ID NO: 2666) CEP290-1858 - GAUGUAGAUUGAGGUAGAAUC 21 downstream (SEQ ID NO: 2667) CEP290-1859 - GUAGAUUGAGGUAGAAUC 18 downstream (SEQ ID NO: 2668) CEP290-1860 + GAAUGAUCAUUCUUGUGGCAGUA 23 downstream (SEQ ID NO: 2669) CEP290-1861 + GAUCAUUCUUGUGGCAGUA 19 downstream (SEQ ID NO: 2670) CEP290-1862 + GAAUGAUCAUUCUUGUGGCAGU 22 downstream (SEQ ID NO: 2671) CEP290-1863 + GAUCAUUCUUGUGGCAGU 18 downstream (SEQ ID NO: 2672) CEP290-1864 - GAGAGGUAAAGGUUCAUGAGAC 22 downstream (SEQ ID NO: 2673) CEP290-1865 - GAGGUAAAGGUUCAUGAGAC 20 downstream (SEQ ID NO: 2674) CEP290-1866 - GGUAAAGGUUCAUGAGAC 18 downstream (SEQ ID NO: 2675) CEP290-1867 + GGUAGCUUUUGACAGUUUUUAAG 23 downstream (SEQ ID NO: 2676) CEP290-1868 + GUAGCUUUUGACAGUUUUUAAG 22 downstream (SEQ ID NO: 2677) CEP290-1869 + GCUUUUGACAGUUUUUAAG 19 downstream (SEQ ID NO: 2678) CEP290-1870 + GUAGCUUUUGACAGUUUUUAAGGC 24 downstream (SEQ ID NO: 2679) CEP290-1871 + GCUUUUGACAGUUUUUAAGGC 21 downstream (SEQ ID NO: 2680) CEP290-1872 + GAAAUUCACUGAGCAAAACAAC 22 downstream (SEQ ID NO: 2681) CEP290-1873 + GUGGCAGUAAGGAGGAUGUAAGA 23 downstream (SEQ ID NO: 2682) CEP290-1874 + GGCAGUAAGGAGGAUGUAAGA 21 downstream (SEQ ID NO: 2683) CEP290-1875 + GCAGUAAGGAGGAUGUAAGA 20 downstream (SEQ ID NO: 775) CEP290-1876 - GGAAAUUAUUGUUGCUUUUU 20 downstream (SEQ ID NO: 2685) CEP290-1877 - GAAAUUAUUGUUGCUUUUU 19 downstream (SEQ ID NO: 2686) CEP290-1878 - GAAAAACUUGAAAUUUGAUAG 21 downstream (SEQ ID NO: 2687) CEP290-1879 - GAAGAAAAAAGAAAUAGAUGUAGA 24 downstream (SEQ ID NO: 2688) CEP290-1880 - GAAAAAAGAAAUAGAUGUAGA 21 downstream (SEQ ID NO: 2689) CEP290-1881 - GUGUUGCCCAGGCUGGAGUGCA 22 downstream (SEQ ID NO: 2690) CEP290-1882 - GUUGCCCAGGCUGGAGUGCA 20 downstream (SEQ ID NO: 2691) CEP290-1883 - GAGUCUCACUGUGUUGCCCAGG 22 downstream (SEQ ID NO: 2692) CEP290-1884 - GUCUCACUGUGUUGCCCAGG 20 downstream (SEQ ID NO: 2693) CEP290-1885 + UUUUUAAGGCGGGGAGUCACA 21 downstream (SEQ ID NO: 2694) CEP290-1886 + UUUUAAGGCGGGGAGUCACA 20 downstream (SEQ ID NO: 672) CEP290-1887 + UUUAAGGCGGGGAGUCACA 19 downstream (SEQ ID NO: 2696) CEP290-1888 + UUAAGGCGGGGAGUCACA 18 downstream (SEQ ID NO: 2697) CEP290-1889 - UGUCAAAAGCUACCGGUUAC 20 downstream (SEQ ID NO: 757) CEP290-1890 - UCAAAAGCUACCGGUUAC 18 downstream (SEQ ID NO: 2699) CEP290-1891 + UUCAUCUCUUGCUCUAGAUGAC 22 downstream (SEQ ID NO: 2700) CEP290-1892 + UCAUCUCUUGCUCUAGAUGAC 21 downstream (SEQ ID NO: 2701) CEP290-1893 + UCUCUUGCUCUAGAUGAC 18 downstream (SEQ ID NO: 2702) CEP290-1894 - UCACGAAAAUCAGAUUUCAUGU 22 downstream (SEQ ID NO: 2703) CEP290-1895 - UAAUACAUGAGAGUGAUUAGUG 22 downstream (SEQ ID NO: 2704) CEP290-1896 - UACAUGAGAGUGAUUAGUG 19 downstream (SEQ ID NO: 2705) CEP290-1897 + UAUUAGCUUGAACUCUGUGCCAAA 24 downstream (SEQ ID NO: 2706) CEP290-1898 + UUAGCUUGAACUCUGUGCCAAA 22 downstream (SEQ ID NO: 2707) CEP290-1899 + UAGCUUGAACUCUGUGCCAAA 21 downstream (SEQ ID NO: 2708) CEP290-1900 + UUGCUCUAGAUGACAUGAGGUAAG 24 downstream (SEQ ID NO: 2709) CEP290-1901 + UGCUCUAGAUGACAUGAGGUAAG 23 downstream (SEQ ID NO: 2710) CEP290-1902 + UCUAGAUGACAUGAGGUAAG 20 downstream (SEQ ID NO: 888) CEP290-1903 + UAGAUGACAUGAGGUAAG 18 downstream (SEQ ID NO: 2712) CEP290-1904 - UGUAGAUUGAGGUAGAAUCAAG 22 downstream (SEQ ID NO: 2713) CEP290-1905 - UAGAUUGAGGUAGAAUCAAG 20 downstream (SEQ ID NO: 2714) CEP290-1906 + UAUAAGAUGCAGAACUAGUGUAGA 24 downstream (SEQ ID NO: 2715) CEP290-1907 + UAAGAUGCAGAACUAGUGUAGA 22 downstream (SEQ ID NO: 2716) CEP290-1908 - UAGAUGUAGAUUGAGGUAGAAUC 23 downstream (SEQ ID NO: 2717) CEP290-1909 - UGUAGAUUGAGGUAGAAUC 19 downstream (SEQ ID NO: 2718) CEP290-1910 + UGAUCAUUCUUGUGGCAGUA 20 downstream (SEQ ID NO: 688) CEP290-1911 + UAGAAUGAUCAUUCUUGUGGCAGU 24 downstream (SEQ ID NO: 2720) CEP290-1912 + UGAUCAUUCUUGUGGCAGU 19 downstream (SEQ ID NO: 2721) CEP290-1913 - UUGAGAGGUAAAGGUUCAUGAGAC 24 downstream (SEQ ID NO: 2722) CEP290-1914 - UGAGAGGUAAAGGUUCAUGAGAC 23 downstream (SEQ ID NO: 2723) CEP290-1915 + UAGCUUUUGACAGUUUUUAAG 21 downstream (SEQ ID NO: 2724) CEP290-1916 + UAGCUUUUGACAGUUUUUAAGGC 23 downstream (SEQ ID NO: 2725) CEP290-1917 + UUUUGACAGUUUUUAAGGC 19 downstream (SEQ ID NO: 2726) CEP290-1918 + UUUGACAGUUUUUAAGGC 18 downstream (SEQ ID NO: 2727) CEP290-1919 + UAGAAAUUCACUGAGCAAAACAAC 24 downstream (SEQ ID NO: 2728) CEP290-1920 + UUCACUGAGCAAAACAAC 18 downstream (SEQ ID NO: 2729) CEP290-1921 + UGUGGCAGUAAGGAGGAUGUAAGA 24 downstream (SEQ ID NO: 2730) CEP290-1922 + UGGCAGUAAGGAGGAUGUAAGA 22 downstream (SEQ ID NO: 2731) CEP290-1923 + UAUCAAAAGACUUAUAUUCCAUUA 24 downstream (SEQ ID NO: 2732) CEP290-1924 + UCAAAAGACUUAUAUUCCAUUA 22 downstream (SEQ ID NO: 2733) CEP290-1925 - UUAGGAAAUUAUUGUUGCUUUUU 23 downstream (SEQ ID NO: 2734) CEP290-1926 - UAGGAAAUUAUUGUUGCUUUUU 22 downstream (SEQ ID NO: 2735) CEP290-1927 - UGUGUUGCCCAGGCUGGAGUGCA 23 downstream (SEQ ID NO: 2736) CEP290-1928 - UGUUGCCCAGGCUGGAGUGCA 21 downstream (SEQ ID NO: 2737) CEP290-1929 - UUGCCCAGGCUGGAGUGCA 19 downstream (SEQ ID NO: 2738) CEP290-1930 - UGCCCAGGCUGGAGUGCA 18 downstream (SEQ ID NO: 2739) CEP290-1931 - UCUCACUGUGUUGCCCAGG 19 downstream (SEQ ID NO: 2740) CEP290-13 + AUGAGAUACUCACAAUUACAAC 22 upstream (SEQ ID NO: 1049) CEP290-18 + GUAUGAGAUACUCACAAUUACAAC 24 upstream (SEQ ID NO: 1051) CEP290-14 + UAUGAGAUACUCACAAUUACAAC 23 upstream (SEQ ID NO: 1053) CEP290-19 + GGUAUGAGAUAUUCACAAUUACAA 24 upstream (SEQ ID NO: 1057)

Table 10A provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the first tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, have good orthogonality, and start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a N. meningitidis Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 10A  Position relative gRNA  DNA Target Site to Name Strand Targeting Domain Length mutation CEP290- + GGCAAAAGCAGCAGAAAGC 20 upstream 1932 A (SEQ ID NO: 591) CEP290- − GUGGCUGAAUGACUUCU 17 upstream 1933 (SEQ ID NO: 592) CEP290- − GUUGUUCUGAGUAGCUU 17 upstream 1934 (SEQ ID NO: 590) CEP290- − GACUAGAGGUCACGAAA 17 downstream 1935 (SEQ ID NO: 593) CEP290- − GAGUUCAAGCUAAUACAUG 20 downstream 1936 A (SEQ ID NO: 589)

Table 10B provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene selected according to the second tier parameters. The targeting domains are within 1000 bp upstream of an Alu repeat, within 40 bp upstream of mutation, or 1000 bp downstream of the mutation, have good orthogonality, and do not start with G. It is contemplated herein that the targeting domain hybridizes to the target domain through complementary base pairing. Any of the targeting domains in the table can be used with a N. meningitidis Cas9 molecule that generates a double stranded break (Cas9 nuclease) or a single-stranded break (Cas9 nickase).

TABLE 10B  Target Position DNA Site relative to gRNA Name Strand Targeting Domain Length mutation CEP290-1937 + AAAAGCAGCAGAAAGCA 17 upstream (SEQ ID NO: 1012) CEP290-1938 − AACGUUGUUCUGAGUAGCUU 20 upstream (SEQ ID NO: 1014) CEP290-1939 − AAUAGAGGCUUAUGGAU 17 upstream (SEQ ID NO: 1007) CEP290-1940 + ACUUAAUGAGUGCUUCCCUC 20 upstream (SEQ ID NO: 2748) CEP290-1941 − AGAAAUAGAGGCUUAUGGA 20 upstream U (SEQ ID NO: 1016) CEP290-1942 + AGCAGAAAGCAAACUGA 17 upstream (SEQ ID NO: 1011) CEP290-1943 + AGCAGCAGAAAGCAAACUGA 20 upstream (SEQ ID NO: 1018) CEP290-1944 + AGGGUCUGGUCCAUAUU 17 upstream (SEQ ID NO: 2752) CEP290-1945 − AUAGUGGCUGAAUGACUUCU 20 upstream (SEQ ID NO: 2753) CEP290-1946 + AUGUCUGGUUAAAAGAG 17 upstream (SEQ ID NO: 2754) CEP290-1947 + CAAAGGGUCUGGUCCAUAUU 20 upstream (SEQ ID NO: 2755) CEP290-1948 − CAUCAGAAAUAGAGGCU 17 upstream (SEQ ID NO: 1009) CEP290-1949 − CCUCAUCAGAAAUAGAGGCU 20 upstream (SEQ ID NO: 1017) CEP290-1950 − CUGAGGACAGAACAAGC 17 upstream (SEQ ID NO: 1008) CEP290-1951 − CUGCUGCUUUUGCCAAAGAG 20 upstream (SEQ ID NO: 725) CEP290-1952 − CUGCUUUUGCCAAAGAG 17 upstream (SEQ ID NO: 711) CEP290-1953 + UAAUGAGUGCUUCCCUC 17 upstream (SEQ ID NO: 2761) CEP290-1954 + UAGAUGUCUGGUUAAAAGA 20 upstream G (SEQ ID NO: 2762) CEP290-1955 − UCAUUCUCCUUAGGUCACUU 20 upstream (SEQ ID NO: 2763) CEP290-1956 − UUACUGAGGACAGAACAAGC 20 upstream (SEQ ID NO: 1013) CEP290-1957 − UUCUCCUUAGGUCACUU 17 upstream (SEQ ID NO: 2765) CEP290-1958 − AAGAAAAAAGAAAUAGA 17 downstream (SEQ ID NO: 2766) CEP290-1959 − AGAUUGAGGUAGAAUCAAG 20 downstream A (SEQ ID NO: 2767) CEP290-1960 + AGUCACAUGGGAGUCACAGG 20 downstream (SEQ ID NO: 1006) CEP290-1961 + CAAAAAAAGAAUCCUCU 17 downstream (SEQ ID NO: 2769) CEP290-1962 + CAACAAAAAAAGAAUCCUCU 20 downstream (SEQ ID NO: 2770) CEP290-1963 + CACAUGGGAGUCACAGG 17 downstream (SEQ ID NO: 1005) CEP290-1964 + CAUUCUUCACACAUGAA 17 downstream (SEQ ID NO: 2772) CEP290-1965 − UAGAAGAAAAAAGAAAUAG 20 downstream A (SEQ ID NO: 2773) CEP290-1966 − UGAGACUAGAGGUCACGAAA 20 downstream (SEQ ID NO: 2774) CEP290-1967 − UUCAAGCUAAUACAUGA 17 downstream (SEQ ID NO: 1004) CEP290-1968 + UUCCAUUCUUCACACAUGAA 20 downstream (SEQ ID NO: 2776) CEP290-1969 − UUGAGGUAGAAUCAAGA 17 downstream (SEQ ID NO: 2777)

Table 11 provides targeting domains for break-induced deletion of genomic sequence including the mutation at the LCA10 target position in the CEP290 gene by dual targeting (e.g., dual double strand cleavage). Exemplary gRNA pairs to be used with S. aureus Cas9 are shown in Table 11, e.g., CEP290-323 can be combined with CEP290-11, CEP290-323 can be combined with CEP290-64, CEP290-490 can be combined with CEP290-496, CEP290-490 can be combined with CEP290-502, CEP290-490 can be combined with CEP290-504, CEP290-492 can be combined with CEP290-502, or CEP290-492 can be combined with CEP290-504.

TABLE 11  Upstream gRNA (SEQ ID NO) Downstream gRNA (SEQ ID NO) CEP290-323 GTTCTGTCCTCAGTAAAAGGTA CEP290-11 GACACTGCCAATAGGG (SEQ ID NO: 389) ATAGGT (corresponding RNA  (SEQ ID NO: 387) sequence in (corresponding RNA SEQ ID NO: 530) sequence in SEQ ID NO: 1047) CEP290-323 GTTCTGTCCTCAGTAAAAGGTA CEP290-64 GTCAAAAGCTACCGGT (SEQ ID NO: 389) TACCTG (SEQ ID NO: 388) (corresponding RNA sequence in SEQ ID NO: 558) CEP290-490 GAATAGTTTGTTCTGGGTAC CEP290-496 GATGCAGAACTAGTGT (SEQ ID NO: 390) AGAC (SEQ ID NO: 392) (corresponding  (corresponding RNA RNA sequence in sequence in SEQ ID NO: SEQ ID NO: 468) 460) CEP290-490 GAATAGTTTGTTCTGGGTAC CEP290-502 GTCACATGGGAGTCAC (SEQ ID NO: 390) AGGG (SEQ ID NO: 393) (corresponding RNA sequence in SEQ ID NO: 586) CEP290-490 GAATAGTTTGTTCTGGGTAC CEP290-504 GAGTATCTCCTGTTTGG (SEQ ID NO: 390) CA (SEQ ID NO: 394) (corresponding RNA sequence in SEQ ID NO: 568) CEP290-492 GAGAAAGGGATGGGCACTTA CEP290-502 GTCACATGGGAGTCAC (SEQ ID NO: 391) AGGG (corresponding  (SEQ ID NO: 393) RNA sequence in SEQ ID NO: 538) CEP290-492 GAGAAAGGGATGGGCACTTA CEP290-504 GAGTATCTCCTGTTTGG (SEQ ID NO: 391) CA (SEQ ID NO: 394)

IV. RNA-Guided Nucleases

RNA-guided nucleases according to the present disclosure include, without limitation, naturally-occurring Class 2 CRISPR nucleases such as Cas9, and Cpf1, as well as other nucleases derived or obtained therefrom. In functional terms, RNA-guided nucleases are defined as those nucleases that: (a) interact with (e.g., complex with) a gRNA; and (b) together with the gRNA, associate with, and optionally cleave or modify, a target region of a DNA that includes (i) a sequence complementary to the targeting domain of the gRNA and, optionally, (ii) an additional sequence referred to as a “protospacer adjacent motif,” or “PAM,” which is described in greater detail below. As the following examples will illustrate, RNA-guided nucleases can be defined, in broad terms, by their PAM specificity and cleavage activity, even though variations may exist between individual RNA-guided nucleases that share the same PAM specificity or cleavage activity. Skilled artisans will appreciate that some aspects of the present disclosure relate to systems, methods and compositions that can be implemented using any suitable RNA-guided nuclease having a certain PAM specificity and/or cleavage activity. For this reason, unless otherwise specified, the term RNA-guided nuclease should be understood as a generic term, and not limited to any particular type (e.g., Cas9 vs. Cpf1), species (e.g., S. pyogenes vs. S. aureus) or variation (e.g., full-length vs. truncated or split; naturally-occurring PAM specificity vs. engineered PAM specificity).

Turning to the PAM sequence, this structure takes its name from its sequential relationship to the “protospacer” sequence that is complementary to gRNA targeting domains (or “spacers”). Together with protospacer sequences, PAM sequences define target regions or sequences for specific RNA-guided nuclease/gRNA combinations.

Various RNA-guided nucleases may require different sequential relationships between PAMs and protospacers. In general, Cas9s recognize PAM sequences that are 5′ of the protospacer as visualized relative to the top or complementary strand.

In addition to recognizing specific sequential orientations of PAMs and protospacers, RNA-guided nucleases generally recognize specific PAM sequences. S. aureus Cas9, for example, recognizes a PAM sequence of NNGRRT, wherein the N sequences are immediately 3′ of the region recognized by the gRNA targeting domain. S. pyogenes Cas9 recognizes NGG PAM sequences. It should also be noted that engineered RNA-guided nucleases can have PAM specificities that differ from the PAM specificities of similar nucleases (such as the naturally occurring variant from which an RNA-guided nuclease is derived, or the naturally occurring variant having the greatest amino acid sequence homology to an engineered RNA-guided nuclease). Modified Cas9s that recognize alternate PAM sequences are described below.

RNA-guided nucleases are also characterized by their DNA cleavage activity: naturally-occurring RNA-guided nucleases typically form DSBs in target nucleic acids, but engineered variants have been produced that generate only SSBs (discussed above; see also Ran 2013, incorporated by reference herein), or that do not cut at all.

Cas9 Molecules

Crystal structures have been determined for S. pyogenes Cas9 (Jinek 2014), and for S. aureus Cas9 in complex with a unimolecular gRNA and a target DNA (Nishimasu 2014; Anders 2014; and Nishimasu 2015).

Cas9 molecules of a variety of species can be used in the methods and compositions described herein. While the S. pyogenes, S. aureus, and S. thermophilus Cas9 molecules are the subject of much of the disclosure herein, Cas9 molecules of, derived from, or based on the Cas9 proteins of other species listed herein can be used as well. In other words, while the much of the description herein uses S. pyogenes and S. thermophilus Cas9 molecules Cas9 molecules from the other species can replace them. Such species include: Acidovorax avenae, Actinobacillus pleuropneumoniae, Actinobacillus succinogenes, Actinobacillus suis, Actinomyces sp., Cycliphilusdenitrificans, Aminomonas paucivorans, Bacillus cereus, Bacillus smithii, Bacillus thuringiensis, Bacteroides sp., Blastopirellula marina, Bradyrhizobium sp., Brevibacillus laterosporus, Campylobacter coli, Campylobacter jejuni, Campylobacter lari, Candidatus puniceispirillum, Clostridium cellulolyticum, Clostridium perfringens, Corynebacterium accolens, Corynebacterium diphtheria, Corynebacterium matruchotii, Dinoroseobacter shibae, Eubacterium dolichum, Gammaproteobacterium, Gluconacetobacter diazotrophicus, Haemophilus parainfluenzae, Haemophilus sputorum, Helicobacter canadensis, Helicobacter cinaedi, Helicobacter mustelae, Ilyobacter polytropus, Kingella kingae, Lactobacillus crispatus, Listeria ivanovii, Listeria monocytogenes, Listeriaceae bacterium, Methylocystis sp., Methylosinus trichosporium, Mobiluncus mulieris, Neisseria bacilliformis, Neisseria cinerea, Neisseria flavescens, Neisseria lactamica, Neisseria meningitidis, Neisseria sp., Neisseria wadsworthii, Nitrosomonas sp., Parvibaculum lavamentivorans, Pasteurella multocida, Phascolarctobacterium succinatutens, Ralstonia syzygii, Rhodopseudomonas palustris, Rhodovulum sp., Simonsiella muelleri, Sphingomonas sp., Sporolactobacillus vineae, Staphylococcus aureus, Staphylococcus lugdunensis, Streptococcus sp., Subdoligranulum sp., Tistrella mobilis, Treponema sp., or Verminephrobacter eiseniae.

A Cas9 molecule, or Cas9 polypeptide, as that term is used herein, refers to a molecule or polypeptide that can interact with a guide RNA (gRNA) molecule and, in concert with the gRNA molecule, homes or localizes to a site which comprises a target domain and PAM sequence. Cas9 molecule and Cas9 polypeptide, as those terms are used herein, refer to naturally occurring Cas9 molecules and to engineered, altered, or modified Cas9 molecules or Cas9 polypeptides that differ, e.g., by at least one amino acid residue, from a reference sequence, e.g., the most similar naturally occurring Cas9 molecule or a sequence of Table 12.

Cas9 Domains

Crystal structures have been determined for two different naturally occurring bacterial Cas9 molecules (Jinek 2014) and for S. pyogenes Cas9 with a guide RNA (e.g., a synthetic fusion of crRNA and tracrRNA) (Nishimasu 2014; Anders 2014).

A naturally occurring Cas9 molecule comprises two lobes: a recognition (REC) lobe and a nuclease (NUC) lobe; each of which further comprises domains described herein. FIGS. 8A-8B provide a schematic of the organization of important Cas9 domains in the primary structure. The domain nomenclature and the numbering of the amino acid residues encompassed by each domain used throughout this disclosure is as described in Nishimasu 2014. The numbering of the amino acid residues is with reference to Cas9 from S. pyogenes.

The REC lobe comprises the arginine-rich bridge helix (BH), the REC1 domain, and the REC2 domain. The REC lobe does not share structural similarity with other known proteins, indicating that it is a Cas9-specific functional domain. The BH domain is a long α helix and arginine rich region and comprises amino acids 60-93 of the sequence of S. pyogenes Cas9. The REC1 domain is important for recognition of the repeat:anti-repeat duplex, e.g., of a gRNA or a tracrRNA, and is therefore critical for Cas9 activity by recognizing the target sequence. The REC1 domain comprises two REC1 motifs at amino acids 94 to 179 and 308 to 717 of the sequence of S. pyogenes Cas9. These two REC1 domains, though separated by the REC2 domain in the linear primary structure, assemble in the tertiary structure to form the REC1 domain. The REC2 domain, or parts thereof, may also play a role in the recognition of the repeat:anti-repeat duplex. The REC2 domain comprises amino acids 180-307 of the sequence of S. pyogenes Cas9.

The NUC lobe comprises the RuvC domain (also referred to herein as RuvC-like domain), the HNH domain (also referred to herein as HNH-like domain), and the PAM-interacting (PI) domain. The RuvC domain shares structural similarity to retroviral integrase superfamily members and cleaves a single strand, e.g., the non-complementary strand of the target nucleic acid molecule. The RuvC domain is assembled from the three split RuvC motifs (RuvC I, RuvCII, and RuvCIII, which are often commonly referred to in the art as RuvCI domain, or N-terminal RuvC domain, RuvCII domain, and RuvCIII domain) at amino acids 1-59, 718-769, and 909-1098, respectively, of the sequence of S. pyogenes Cas9. Similar to the REC1 domain, the three RuvC motifs are linearly separated by other domains in the primary structure, however in the tertiary structure, the three RuvC motifs assemble and form the RuvC domain. The HNH domain shares structural similarity with HNH endonucleases, and cleaves a single strand, e.g., the complementary strand of the target nucleic acid molecule. The HNH domain lies between the RuvC II-III motifs and comprises amino acids 775-908 of the sequence of S. pyogenes Cas9. The PI domain interacts with the PAM of the target nucleic acid molecule, and comprises amino acids 1099-1368 of the sequence of S. pyogenes Cas9.

RuvC-Like Domain and HNH-Like Domain

In an embodiment, a Cas9 molecule or Cas9 polypeptide comprises an HNH-like domain and a RuvC-like domain. In an embodiment, cleavage activity is dependent on a RuvC-like domain and an HNH-like domain. A Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, can comprise one or more of the following domains: a RuvC-like domain and an HNH-like domain. In an embodiment, a Cas9 molecule or Cas9 polypeptide is an eaCas9 molecule or eaCas9 polypeptide and the eaCas9 molecule or eaCas9 polypeptide comprises a RuvC-like domain, e.g., a RuvC-like domain described below, and/or an HNH-like domain, e.g., an HNH-like domain described below.

RuvC-Like Domains

In an embodiment, a RuvC-like domain cleaves, a single strand, e.g., the non-complementary strand of the target nucleic acid molecule. The Cas9 molecule or Cas9 polypeptide can include more than one RuvC-like domain (e.g., one, two, three or more RuvC-like domains). In an embodiment, a RuvC-like domain is at least 5, 6, 7, 8 amino acids in length but not more than 20, 19, 18, 17, 16 or 15 amino acids in length. In an embodiment, the Cas9 molecule or Cas9 polypeptide comprises an N-terminal RuvC-like domain of about 10 to 20 amino acids, e.g., about 15 amino acids in length.

N-Terminal RuvC-Like Domains

Some naturally occurring Cas9 molecules comprise more than one RuvC-like domain with cleavage being dependent on the N-terminal RuvC-like domain. Accordingly, Cas9 molecules or Cas9 polypeptide can comprise an N-terminal RuvC-like domain. Exemplary N-terminal RuvC-like domains are described below.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an N-terminal RuvC-like domain comprising an amino acid sequence of formula I:

(SEQ ID NO: 8) D-X1-G-X2-X3-X4-X5-G-X6-X7-X8-X9, 

wherein,

X1 is selected from I, V, M, L and T (e.g., selected from I, V, and L);

X2 is selected from T, I, V, S, N, Y, E and L (e.g., selected from T, V, and I);

X3 is selected from N, S, G, A, D, T, R, M and F (e.g., A or N);

X4 is selected from S, Y, N and F (e.g., S);

X5 is selected from V, I, L, C, T and F (e.g., selected from V, I and L);

X6 is selected from W, F, V, Y, S and L (e.g., W);

X7 is selected from A, S, C, V and G (e.g., selected from A and S);

X8 is selected from V, I, L, A, M and H (e.g., selected from V, I, M and L); and

X9 is selected from any amino acid or is absent, designated by Δ (e.g., selected from T, V, I, L, Δ, F, S, A, Y, M and R, or, e.g., selected from T, V, I, L and Δ).

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of SEQ ID NO: 8, by as many as 1 but no more than 2, 3, 4, or 5 residues.

In embodiment, the N-terminal RuvC-like domain is cleavage competent.

In embodiment, the N-terminal RuvC-like domain is cleavage incompetent.

In an embodiment, a eaCas9 molecule or eaCas9 polypeptide comprises an N-terminal RuvC-like domain comprising an amino acid sequence of formula II:

(SEQ ID NO: 9) D-X1-G-X2-X3-S-X5-G-X6-X7-X8-X9,, 

wherein

X1 is selected from I, V, M, L and T (e.g., selected from I, V, and L);

X2 is selected from T, I, V, S, N, Y, E and L (e.g., selected from T, V, and I);

X3 is selected from N, S, G, A, D, T, R, M and F (e.g., A or N);

X5 is selected from V, I, L, C, T and F (e.g., selected from V, I and L);

X6 is selected from W, F, V, Y, S and L (e.g., W);

X7 is selected from A, S, C, V and G (e.g., selected from A and S);

X8 is selected from V, I, L, A, M and H (e.g., selected from V, I, M and L); and

X9 is selected from any amino acid or is absent (e.g., selected from T, V, I, L, Δ, F, S, A, Y, M and R or selected from e.g., T, V, I, L and Δ).

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of SEQ ID NO:9 by as many as 1 but no more than 2, 3, 4, or 5 residues.

In an embodiment, the N-terminal RuvC-like domain comprises an amino acid sequence of formula III:

(SEQ ID NO: 10) D-I-G-X2-X3-S-V-G-W-A-X8-X9,

wherein

X2 is selected from T, I, V, S, N, Y, E and L (e.g., selected from T, V, and I);

X3 is selected from N, S, G, A, D, T, R, M and F (e.g., A or N);

X8 is selected from V, I, L, A, M and H (e.g., selected from V, I, M and L); and

X9 is selected from any amino acid or is absent (e.g., selected from T, V, I, L, Δ, F, S, A, Y, M and R or selected from e.g., T, V, I, L and Δ).

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of SEQ ID NO: 10 by as many as 1 but no more than, 2, 3, 4, or 5 residues.

In an embodiment, the N-terminal RuvC-like domain comprises an amino acid sequence of formula III:

(SEQ ID NO: 11) D-I-G-T-N-S-V-G-W-A-V-X,

wherein

X is a non-polar alkyl amino acid or a hydroxyl amino acid, e.g., X is selected from V, I, L and T (e.g., the eaCas9 molecule can comprise an N-terminal RuvC-like domain shown in FIGS. 2A-2G (is depicted as Y)).

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of SEQ ID NO: 11 by as many as 1 but no more than, 2, 3, 4, or 5 residues.

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of an N-terminal RuvC like domain disclosed herein, e.g., in FIGS. 3A-3B or FIGS. 7A-7B, as many as 1 but no more than 2, 3, 4, or 5 residues. In an embodiment, 1, 2, or all 3 of the highly conserved residues identified in FIGS. 3A-3B or FIGS. 7A-7B are present.

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of an N-terminal RuvC-like domain disclosed herein, e.g., in FIGS. 4A-4B or FIGS. 7A-7B, as many as 1 but no more than 2, 3, 4, or 5 residues. In an embodiment, 1, 2, 3 or all 4 of the highly conserved residues identified in FIGS. 4A-4B or FIGS. 7A-7B are present.

Additional RuvC-Like Domains

In addition to the N-terminal RuvC-like domain, the Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, can comprise one or more additional RuvC-like domains. In an embodiment, the Cas9 molecule or Cas9 polypeptide can comprise two additional RuvC-like domains. Preferably, the additional RuvC-like domain is at least 5 amino acids in length and, e.g., less than 15 amino acids in length, e.g., 5 to 10 amino acids in length, e.g., 8 amino acids in length.

An additional RuvC-like domain can comprise an amino acid sequence:

I-X1-X2-E-X3-A-R-E (SEQ ID NO: 12), wherein

X1 is V or H,

X2 is I, L or V (e.g., I or V); and

X3 is M or T.

In an embodiment, the additional RuvC-like domain comprises the amino acid sequence:

I-V-X2-E-M-A-R-E (SEQ ID NO: 13), wherein

X2 is I, L or V (e.g., I or V) (e.g., the eaCas9 molecule or eaCas9 polypeptide can comprise an additional RuvC-like domain shown in FIG. 2A-2G or FIGS. 7A-7B (depicted as B)).

An additional RuvC-like domain can comprise an amino acid sequence:

H-H-A-X1-D-A-X2-X3 (SEQ ID NO: 14), wherein

X1 is H or L;

X2 is R or V; and

X3 is E or V.

In an embodiment, the additional RuvC-like domain comprises the amino acid sequence: H-H-A-H-D-A-Y-L (SEQ ID NO: 15).

In an embodiment, the additional RuvC-like domain differs from a sequence of SEQ ID NOs: 13, 15, 12 or 14 by as many as 1 but no more than 2, 3, 4, or 5 residues.

In some embodiments, the sequence flanking the N-terminal RuvC-like domain is a sequences of formula V:

(SEQ ID NO: 16) K-X1′-Y-X2′-X3′-X4′-Z-T-D-X9′-Y,.

wherein

X1′ is selected from K and P,

X2′ is selected from V, L, I, and F (e.g., V, I and L);

X3′ is selected from G, A and S (e.g., G),

X4′ is selected from L, I, V and F (e.g., L);

X9′ is selected from D, E, N and Q; and

Z is an N-terminal RuvC-like domain, e.g., as described above.

HNH-Like Domains

In an embodiment, an HNH-like domain cleaves a single stranded complementary domain, e.g., a complementary strand of a double stranded nucleic acid molecule. In an embodiment, an HNH-like domain is at least 15, 20, 25 amino acids in length but not more than 40, 35 or 30 amino acids in length, e.g., 20 to 35 amino acids in length, e.g., 25 to 30 amino acids in length. Exemplary HNH-like domains are described below.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an HNH-like domain having an amino acid sequence of formula VI:

X1-X2-X3-H-X4-X5-P X6 X7 X8 X9 X10 X11 X12 X13 X14 X15 N-X16-X17-X18-X19-X20-X21-X22-X23-N (SEQ ID NO: 17), wherein

X1 is selected from D, E, Q and N (e.g., D and E);

X2 is selected from L, I, R, Q, V, M and K;

X3 is selected from D and E;

X4 is selected from I, V, T, A and L (e.g., A, I and V);

X5 is selected from V, Y, I, L, F and W (e.g., V, I and L);

X6 is selected from Q, H, R, K, Y, I, L, F and W;

X7 is selected from S, A, D, T and K (e.g., S and A);

X8 is selected from F, L, V, K, Y, M, I, R, A, E, D and Q (e.g., F);

X9 is selected from L, R, T, I, V, S, C, Y, K, F and G;

X10 is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

X11 is selected from D, S, N, R, L and T (e.g., D);

X12 is selected from D, N and S;

X13 is selected from S, A, T, G and R (e.g., S);

X14 is selected from I, L, F, S, R, Y, Q, W, D, K and H (e.g., I, L and F);

X15 is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y and V;

X16 is selected from K, L, R, M, T and F (e.g., L, R and K);

X17 is selected from V, L, I, A and T;

X18 is selected from L, I, V and A (e.g., L and I);

X19 is selected from T, V, C, E, S and A (e.g., T and V);

X20 is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H and A;

X21 is selected from S, P, R, K, N, A, H, Q, G and L;

X22 is selected from D, G, T, N, S, K, A, I, E, L, Q, R and Y; and

X23 is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D and F.

In an embodiment, a HNH-like domain differs from a sequence of SEQ ID NO: 16 by at least one but no more than, 2, 3, 4, or 5 residues.

In an embodiment, the HNH-like domain is cleavage competent.

In an embodiment, the HNH-like domain is cleavage incompetent.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an HNH-like domain comprising an amino acid sequence of formula VII:

(SEQ ID NO: 18) X1-X2-X3-H-X4-X5-P-X6-S-X8-X9-X10-D-D-S-X14-X15-N- K-V-L-X19-X20-X21-X22-X23-N,

wherein

X1 is selected from D and E;

X2 is selected from L, I, R, Q, V, M and K;

X3 is selected from D and E;

X4 is selected from I, V, T, A and L (e.g., A, I and V);

X5 is selected from V, Y, I, L, F and W (e.g., V, I and L);

X6 is selected from Q, H, R, K, Y, I, L, F and W;

X8 is selected from F, L, V, K, Y, M, I, R, A, E, D and Q (e.g., F);

X9 is selected from L, R, T, I, V, S, C, Y, K, F and G;

X10 is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

X14 is selected from I, L, F, S, R, Y, Q, W, D, K and H (e.g., I, L and F);

X15 is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y and V;

X19 is selected from T, V, C, E, S and A (e.g., T and V);

X20 is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H and A;

X21 is selected from S, P, R, K, N, A, H, Q, G and L;

X22 is selected from D, G, T, N, S, K, A, I, E, L, Q, R and Y; and

X23 is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D and F.

In an embodiment, the HNH-like domain differs from a sequence of SEQ ID NO: 15 by 1, 2, 3, 4, or 5 residues.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an HNH-like domain comprising an amino acid sequence of formula VII:

(SEQ ID NO: 19) X1-V-X3-H-I-V-P-X6-S-X8-X9-X10-D-D-S-X14-X15-N-K-V- L-T-X20-X21-X22-X23-N,

wherein

X1 is selected from D and E;

X3 is selected from D and E;

X6 is selected from Q, H, R, K, Y, I, L and W;

X8 is selected from F, L, V, K, Y, M, I, R, A, E, D and Q (e.g., F);

X9 is selected from L, R, T, I, V, S, C, Y, K, F and G;

X10 is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

X14 is selected from I, L, F, S, R, Y, Q, W, D, K and H (e.g., I, L and F);

X15 is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y and V;

X20 is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H and A;

X21 is selected from S, P, R, K, N, A, H, Q, G and L;

X22 is selected from D, G, T, N, S, K, A, I, E, L, Q, R and Y; and

X23 is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D and F.

In an embodiment, the HNH-like domain differs from a sequence of SEQ ID NO:GG by 1, 2, 3, 4, or 5 residues.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an HNH-like domain having an amino acid sequence of formula VIII:

(SEQ ID NO: 20) D-X2-D-H-I-X5-P-Q-X7-F-X9-X10-D-X12-S-I-D-N-X16-V- L-X19-X20-S-X22-X23-N,

wherein

X2 is selected from I and V;

X5 is selected from I and V;

X7 is selected from A and S;

X9 is selected from I and L;

X10 is selected from K and T;

X12 is selected from D and N;

X16 is selected from R, K and L; X19 is selected from T and V;

X20 is selected from S and R;

X22 is selected from K, D and A; and

X23 is selected from E, K, G and N (e.g., the eaCas9 molecule or eaCas9 polypeptide can comprise an HNH-like domain as described herein).

In an embodiment, the HNH-like domain differs from a sequence of SEQ ID NO: 19 by as many as 1 but no more than 2, 3, 4, or 5 residues.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises the amino acid sequence of formula IX:

(SEQ ID NO: 21) L-Y-Y-L-Q-N-G-X1′-D-M-Y-X2′-X3′-X4′-X5′-L-D-I-X6′- X7′-L-S-X8′-Y-Z-N-R-X9′-K-X10′-D-X11′-V-P,

wherein

X1′ is selected from K and R;

X2′ is selected from V and T;

X3′ is selected from G and D;

X4′ is selected from E, Q and D;

X5′ is selected from E and D;

X6′ is selected from D, N and H;

X7′ is selected from Y, R and N;

X8′ is selected from Q, D and N; X9′ is selected from G and E;

X10′ is selected from S and G;

X11′ is selected from D and N; and

Z is an HNH-like domain, e.g., as described above.

In an embodiment, the eaCas9 molecule or eaCas9 polypeptide comprises an amino acid sequence that differs from a sequence of SEQ ID NO: 21 by as many as 1 but no more than 2, 3, 4, or 5 residues.

In an embodiment, the HNH-like domain differs from a sequence of an HNH-like domain disclosed herein, e.g., in FIGS. 5A-5C or FIGS. 7A-7B, as many as 1 but no more than 2, 3, 4, or 5 residues. In an embodiment, 1 or both of the highly conserved residues identified in FIGS. 5A-5C or FIGS. 7A-7B are present.

In an embodiment, the HNH -like domain differs from a sequence of an HNH-like domain disclosed herein, e.g., in FIGS. 6A-6B or FIGS. 7A-7B , as many as 1 but no more than 2, 3, 4, or 5 residues. In an embodiment, 1, 2, all 3 of the highly conserved residues identified in FIGS. 6A-6B or FIGS. 7A-7B are present.

Cas9 Activities Nuclease and Helicase Activities

In an embodiment, the Cas9 molecule or Cas9 polypeptide is capable of cleaving a target nucleic acid molecule. Typically wild type Cas9 molecules cleave both strands of a target nucleic acid molecule. Cas9 molecules and Cas9 polypeptides can be engineered to alter nuclease cleavage (or other properties), e.g., to provide a Cas9 molecule or Cas9 polypeptide which is a nickase, or which lacks the ability to cleave target nucleic acid. A Cas9 molecule or Cas9 polypeptide that is capable of cleaving a target nucleic acid molecule is referred to herein as an eaCas9 molecule or eaCas9 polypeptide.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises one or more of the following activities:

a nickase activity, i.e., the ability to cleave a single strand, e.g., the non-complementary strand or the complementary strand, of a nucleic acid molecule;

a double stranded nuclease activity, i.e., the ability to cleave both strands of a double stranded nucleic acid and create a double stranded break, which in an embodiment is the presence of two nickase activities;

an endonuclease activity;

an exonuclease activity; and

a helicase activity, i.e., the ability to unwind the helical structure of a double stranded nucleic acid.

In an embodiment, an enzymatically active or eaCas9 molecule or eaCas9 polypeptide cleaves both strands and results in a double stranded break. In an embodiment, an eaCas9 molecule cleaves only one strand, e.g., the strand to which the gRNA hybridizes to, or the strand complementary to the strand the gRNA hybridizes with. In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises cleavage activity associated with an HNH-like domain. In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises cleavage activity associated with an N-terminal RuvC-like domain. In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises cleavage activity associated with an HNH-like domain and cleavage activity associated with an N-terminal RuvC-like domain. In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an active, or cleavage competent, HNH-like domain and an inactive, or cleavage incompetent, N-terminal RuvC-like domain. In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an inactive, or cleavage incompetent, HNH-like domain and an active, or cleavage competent, N-terminal RuvC-like domain.

Some Cas9 molecules or Cas9 polypeptides have the ability to interact with a gRNA molecule, and in conjunction with the gRNA molecule localize to a core target domain, but are incapable of cleaving the target nucleic acid, or incapable of cleaving at efficient rates. Cas9 molecules having no, or no substantial, cleavage activity are referred to herein as an eiCas9 molecule or eiCas9 polypeptide. For example, an eiCas9 molecule or eiCas9 polypeptide can lack cleavage activity or have substantially less, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule or eiCas9 polypeptide, as measured by an assay described herein.

Targeting and PAMs

RNA guided nucleases, such as Cas9 molecules or Cas9 polypeptides, generally, interact with a guide RNA (gRNA) molecule and, in concert with the gRNA molecule, localize to a site which comprises a target domain and a PAM sequence.

In an embodiment, the ability of an eaCas9 molecule or eaCas9 polypeptide to interact with and cleave a target nucleic acid is PAM sequence dependent. A PAM sequence is a sequence in the target nucleic acid. In an embodiment, cleavage of the target nucleic acid occurs upstream from the PAM sequence. EaCas9 molecules from different bacterial species can recognize different sequence motifs (e.g., PAM sequences). In an embodiment, an eaCas9 molecule of S. pyogenes recognizes the sequence motif NGG, NAG, NGA and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Mali 2013. In an embodiment, an eaCas9 molecule of S. thermophilus recognizes the sequence motif NGGNG and NNAGAAW (W=A or T) and directs cleavage of a core target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from these sequences. See, e.g., Horvath 2010 and Deveau 2008. In an embodiment, an eaCas9 molecule of S. mutans recognizes the sequence motif NGG and/or NAAR (R=A or G) and directs cleavage of a core target nucleic acid sequence 1 to 10, e.g., 3 to 5 base pairs, upstream from this sequence. See, e.g., Deveau 2008. In an embodiment, an eaCas9 molecule of S. aureus recognizes the sequence motif NNGRR (R=A or G) and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. In an embodiment, an eaCas9 molecule of S. aureus recognizes the sequence motif NNGRRN (R=A or G) and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. In an embodiment, an eaCas9 molecule of S. aureus recognizes the sequence motif NNGRRT (R=A or G) and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. In an embodiment, an eaCas9 molecule of S. aureus recognizes the sequence motif NNGRRV (R=A or G, V=A, G or C) and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. In an embodiment, an eaCas9 molecule of Neisseria meningitidis recognizes the sequence motif NNNNGATT or NNNGCTT and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Hou 2013. The ability of a Cas9 molecule to recognize a PAM sequence can be determined, e.g., using a transformation assay described in Jinek 2012. In the aforementioned embodiments, N can be any nucleotide residue, e.g., any of A, G, C or T.

As is discussed herein, Cas9 molecules can be engineered to alter the PAM specificity of the Cas9 molecule.

Exemplary naturally occurring Cas9 molecules are described in Chylinski 2013. Such Cas9 molecules include Cas9 molecules of a cluster 1 bacterial family, cluster 2 bacterial family, cluster 3 bacterial family, cluster 4 bacterial family, cluster 5 bacterial family, cluster 6 bacterial family, a cluster 7 bacterial family, a cluster 8 bacterial family, a cluster 9 bacterial family, a cluster 10 bacterial family, a cluster 11 bacterial family, a cluster 12 bacterial family, a cluster 13 bacterial family, a cluster 14 bacterial family, a cluster 15 bacterial family, a cluster 16 bacterial family, a cluster 17 bacterial family, a cluster 18 bacterial family, a cluster 19 bacterial family, a cluster 20 bacterial family, a cluster 21 bacterial family, a cluster 22 bacterial family, a cluster 23 bacterial family, a cluster 24 bacterial family, a cluster 25 bacterial family, a cluster 26 bacterial family, a cluster 27 bacterial family, a cluster 28 bacterial family, a cluster 29 bacterial family, a cluster 30 bacterial family, a cluster 31 bacterial family, a cluster 32 bacterial family, a cluster 33 bacterial family, a cluster 34 bacterial family, a cluster 35 bacterial family, a cluster 36 bacterial family, a cluster 37 bacterial family, a cluster 38 bacterial family, a cluster 39 bacterial family, a cluster 40 bacterial family, a cluster 41 bacterial family, a cluster 42 bacterial family, a cluster 43 bacterial family, a cluster 44 bacterial family, a cluster 45 bacterial family, a cluster 46 bacterial family, a cluster 47 bacterial family, a cluster 48 bacterial family, a cluster 49 bacterial family, a cluster 50 bacterial family, a cluster 51 bacterial family, a cluster 52 bacterial family, a cluster 53 bacterial family, a cluster 54 bacterial family, a cluster 55 bacterial family, a cluster 56 bacterial family, a cluster 57 bacterial family, a cluster 58 bacterial family, a cluster 59 bacterial family, a cluster 60 bacterial family, a cluster 61 bacterial family, a cluster 62 bacterial family, a cluster 63 bacterial family, a cluster 64 bacterial family, a cluster 65 bacterial family, a cluster 66 bacterial family, a cluster 67 bacterial family, a cluster 68 bacterial family, a cluster 69 bacterial family, a cluster 70 bacterial family, a cluster 71 bacterial family, a cluster 72 bacterial family, a cluster 73 bacterial family, a cluster 74 bacterial family, a cluster 75 bacterial family, a cluster 76 bacterial family, a cluster 77 bacterial family, or a cluster 78 bacterial family.

Exemplary naturally occurring Cas9 molecules include a Cas9 molecule of a cluster 1 bacterial family. Examples include a Cas9 molecule of: S. pyogenes (e.g., strain SF370, MGAS10270, MGAS10750, MGAS2096, MGAS315, MGAS5005, MGAS6180, MGAS9429, NZ131 and SSI-1), S. thermophilus (e.g., strain LMD-9), S. pseudoporcinus (e.g., strain SPIN 20026), S. mutans (e.g., strain UA159, NN2025), S. macacae (e.g., strain NCTC11558), S. gallolyticus (e.g., strain UCN34, ATCC BAA-2069), S. equines (e.g., strain ATCC 9812, MGCS 124), S. dysdalactiae (e.g., strain GGS 124), S. bovis (e.g., strain ATCC 700338), S. anginosus (e.g., strain F0211), S. agalactiae (e.g., strain NEM316, A909), Listeria monocytogenes (e.g., strain F6854), Listeria innocua (L. innocua, e.g., strain Clip11262), Enterococcus italicus (e.g., strain DSM 15952), or Enterococcus faecium (e.g., strain 1,231,408). Another exemplary Cas9 molecule is a Cas9 molecule of Neisseria meningitidis (Hou 2013).

In an embodiment, a Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, comprises an amino acid sequence:

having 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with;

differs at no more than, 2, 5, 10, 15, 20, 30, or 40% of the amino acid residues when compared with;

differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than 100, 80, 70, 60, 50, 40 or 30 amino acids from; or

is identical to any Cas9 molecule sequence described herein, or a naturally occurring Cas9 molecule sequence, e.g., a Cas9 molecule from a species listed herein or described in Chylinski 2013; Hou 2013; SEQ ID NOs: 1-4. In an embodiment, the Cas9 molecule or Cas9 polypeptide comprises one or more of the following activities: a nickase activity; a double stranded cleavage activity (e.g., an endonuclease and/or exonuclease activity); a helicase activity; or the ability, together with a gRNA molecule, to home to a target nucleic acid.

In an embodiment, a Cas9 molecule or Cas9 polypeptide comprises the amino acid sequence of the consensus sequence of FIGS. 2A-2G, wherein “*” indicates any amino acid found in the corresponding position in the amino acid sequence of a Cas9 molecule of S. pyogenes, S. thermophilus, S. mutans and L. innocua, and “-” indicates any amino acid. In an embodiment, a Cas9 molecule or Cas9 polypeptide differs from the sequence of the consensus sequence disclosed in FIGS. 2A-2G by at least 1, but no more than 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid residues. In an embodiment, a Cas9 molecule or Cas9 polypeptide comprises the amino acid sequence of SEQ ID NO: 7 of FIGS. 7A-7B, wherein “*” indicates any amino acid found in the corresponding position in the amino acid sequence of a Cas9 molecule of S. pyogenes, or N. meningitidis, “-” indicates any amino acid, and “-” indicates any amino acid or absent. In an embodiment, a Cas9 molecule or Cas9 polypeptide differs from the sequence of SEQ ID NOs: 6 or 7 disclosed in FIGS. 7A-7B by at least 1, but no more than 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid residues.

A comparison of the sequence of a number of Cas9 molecules indicate that certain regions are conserved. These are identified below as:

region 1 (residues 1 to 180, or in the case of region 1′residues 120 to 180)

region 2 (residues360 to 480);

region 3 (residues 660 to 720);

region 4 (residues 817 to 900); and

region 5 (residues 900 to 960);

In an embodiment, a Cas9 molecule or Cas9 polypeptide comprises regions 1-5, together with sufficient additional Cas9 molecule sequence to provide a biologically active molecule, e.g., a Cas9 molecule having at least one activity described herein. In an embodiment, each of regions 1-6, independently, have, 50%, 60%, 70%, or 80% homology with the corresponding residues of a Cas9 molecule or Cas9 polypeptide described herein, e.g., a sequence from FIGS. 2A-2G or from FIGS. 7A-7B.

In an embodiment, a Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, comprises an amino acid sequence referred to as region 1:

having 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 1-180 (the numbering is according to the motif sequence in FIGS. 2A-2G; 52% of residues in the four Cas9 sequences in FIGS. 2A-2G are conserved) of the amino acid sequence of Cas9 of S. pyogenes;

differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than 90, 80, 70, 60, 50, 40 or 30 amino acids from amino acids 1-180 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua; or

is identical to 1-180 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua.

In an embodiment, a Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, comprises an amino acid sequence referred to as region 1′:

having 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 120-180 (55% of residues in the four Cas9 sequences in FIGS. 2A-2G are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 120-180 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua; or

is identical to 120-180 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua.

In an embodiment, a Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, comprises an amino acid sequence referred to as region 2:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 360-480 (52% of residues in the four Cas9 sequences in FIGS. 2A-2G are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 360-480 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua; or

is identical to 360-480 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua.

In an embodiment, a Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, comprises an amino acid sequence referred to as region 3:

having 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homology with amino acids 660-720 (56% of residues in the four Cas9 sequences in FIGS. 2A-2G are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 660-720 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua; or

is identical to 660-720 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua.

In an embodiment, a Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, comprises an amino acid sequence referred to as region 4:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homology with amino acids 817-900 (55% of residues in the four Cas9 sequences in FIGS. 2A-2G are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 817-900 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua; or

is identical to 817-900 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua.

In an embodiment, a Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule or eaCas9 polypeptide, comprises an amino acid sequence referred to as region 5:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homology with amino acids 900-960 (60% of residues in the four Cas9 sequences in FIGS. 2A-2G are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 900-960 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua; or

is identical to 900-960 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or L. innocua.

Modifications of RNA-Guided Nucleases

The RNA-guided nucleases described above have activities and properties that are useful in a variety of applications, but the skilled artisan will appreciate that RNA-guided nucleases may also be modified in certain instances, to alter cleavage activity, PAM specificity, or other structural or functional features.

Turning first to modifications that alter cleavage activity, mutations that reduce or eliminate the activity of domains within the NUC lobe have been described above. As discussed in more detail below, exemplary mutations that may be made in the RuvC domains, in the Cas9 HNH domain, or in the Cpf 1 Nuc domain are described in Ran and Yamano, as well as in Cotta-Ramusino. In general, mutations that reduce or eliminate activity in one of the two nuclease domains result in RNA-guided nucleases with nickase activity, but it should be noted that the type of nickase activity varies depending on which domain is inactivated. As one example, inactivation of a RuvC domain of a Cas9 will result in a nickase that cleaves the complementary strand, while inactivation of a Cas9 HNH domain results in a nickase that cleaves the non-complementary strand.

Modifications of PAM specificity relative to naturally occurring Cas9 reference molecules has been described for both S. pyogenes (Kleinstiver 2015a) and S. aureus (Kleinstiver 2015b). Modifications that improve the targeting fidelity of Cas9 have also been described (Kleinstiver 2016). Each of these references is incorporated by reference herein.

RNA-guided nucleases have been split into two or more parts (see, e.g., Zetsche 2015; Fine 2015; both incorporated by reference).

RNA-guided nucleases are, in some cases, size-optimized or truncated, for example via one or more deletions that reduce the size of the nuclease while still retaining gRNA association, target and PAM recognition, and cleavage activities. In certain embodiments, RNA guided nucleases are bound, covalently or non-covalently, to another polypeptide, nucleotide, or other structure, optionally by means of a linker. RNA-guided nucleases also optionally include a tag, such as a nuclear localization signal to facilitate movement of RNA-guided nuclease protein into the nucleus.

Engineered or Altered Cas9 Molecules and Cas9 Polypeptides

Cas9 molecules and Cas9 polypeptides described herein, e.g., naturally occurring Cas9 molecules, can possess any of a number of properties, including: nickase activity, nuclease activity (e.g., endonuclease and/or exonuclease activity); helicase activity; the ability to associate functionally with a gRNA molecule; and the ability to target (or localize to) a site on a nucleic acid (e.g., PAM recognition and specificity). In an embodiment, a Cas9 molecule or Cas9 polypeptide can include all or a subset of these properties. In typical embodiments, a Cas9 molecule or Cas9 polypeptide has the ability to interact with a gRNA molecule and, in concert with the gRNA molecule, localize to a site in a nucleic acid. Other activities, e.g., PAM specificity, cleavage activity, or helicase activity can vary more widely in Cas9 molecules and Cas9 polypeptides.

Cas9 molecules include engineered Cas9 molecules and engineered Cas9 polypeptides (engineered, as used in this context, means merely that the Cas9 molecule or Cas9 polypeptide differs from a reference sequences, and implies no process or origin limitation). An engineered Cas9 molecule or Cas9 polypeptide can comprise altered enzymatic properties, e.g., altered nuclease activity, (as compared with a naturally occurring or other reference Cas9 molecule) or altered helicase activity. As discussed herein, an engineered Cas9 molecule or Cas9 polypeptide can have nickase activity (as opposed to double strand nuclease activity). In an embodiment an engineered Cas9 molecule or Cas9 polypeptide can have an alteration that alters its size, e.g., a deletion of amino acid sequence that reduces its size, e.g., without significant effect on one or more, or any Cas9 activity. In an embodiment, an engineered Cas9 molecule or Cas9 polypeptide can comprise an alteration that affects PAM recognition. E.g., an engineered Cas9 molecule can be altered to recognize a PAM sequence other than that recognized by the endogenous wild-type PI domain. In an embodiment, a Cas9 molecule or Cas9 polypeptide can differ in sequence from a naturally occurring Cas9 molecule but not have significant alteration in one or more Cas9 activities.

Cas9 molecules or Cas9 polypeptides with desired properties can be made in a number of ways, e.g., by alteration of a parental, e.g., naturally occurring, Cas9 molecules or Cas9 polypeptides, to provide an altered Cas9 molecule or Cas9 polypeptide having a desired property. For example, one or more mutations or differences relative to a parental Cas9 molecule, e.g., a naturally occurring or engineered Cas9 molecule, can be introduced. Such mutations and differences comprise: substitutions (e.g., conservative substitutions or substitutions of non-essential amino acids); insertions; or deletions. In an embodiment, a Cas9 molecule or Cas9 polypeptide can comprises one or more mutations or differences, e.g., at least 1, 2, 3, 4, 5, 10, 15, 20, 30, 40 or 50 mutations, but less than 200, 100, or 80 mutations relative to a reference, e.g., a parental, Cas9 molecule.

In an embodiment, a mutation or mutations do not have a substantial effect on a Cas9 activity, e.g. a Cas9 activity described herein. In an embodiment, a mutation or mutations have a substantial effect on a Cas9 activity, e.g. a Cas9 activity described herein.

Non-Cleaving and Modified-Cleavage Cas9 Molecules and Cas9 Polypeptides

In an embodiment, a Cas9 molecule or Cas9 polypeptide comprises a cleavage property that differs from naturally occurring Cas9 molecules, e.g., that differs from the naturally occurring Cas9 molecule having the closest homology. For example, a Cas9 molecule or Cas9 polypeptide can differ from naturally occurring Cas9 molecules, e.g., a Cas9 molecule of S. pyogenes, as follows: its ability to modulate, e.g., decreased or increased, cleavage of a double stranded nucleic acid (endonuclease and/or exonuclease activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S. pyogenes); its ability to modulate, e.g., decreased or increased, cleavage of a single strand of a nucleic acid, e.g., a non-complementary strand of a nucleic acid molecule or a complementary strand of a nucleic acid molecule (nickase activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S. pyogenes); or the ability to cleave a nucleic acid molecule, e.g., a double stranded or single stranded nucleic acid molecule, can be eliminated.

Modified Cleavage eaCas9 Molecules and eaCas9 Polypeptides

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises one or more of the following activities: cleavage activity associated with an N-terminal RuvC-like domain; cleavage activity associated with an HNH-like domain; cleavage activity associated with an HNH-like domain and cleavage activity associated with an N-terminal RuvC-like domain.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an active, or cleavage competent, HNH-like domain (e.g., an HNH-like domain described herein, e.g., SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, or SEQ ID NO: 21) and an inactive, or cleavage incompetent, N-terminal RuvC-like domain. An exemplary inactive, or cleavage incompetent N-terminal RuvC-like domain can have a mutation of an aspartic acid in an N-terminal RuvC-like domain, e.g., an aspartic acid at position 9 of the consensus sequence disclosed in FIGS. 2A-2G or an aspartic acid at position 10 of SEQ ID NO: 7, e.g., can be substituted with an alanine. In an embodiment, the eaCas9 molecule or eaCas9 polypeptide differs from wild type in the N-terminal RuvC-like domain and does not cleave the target nucleic acid, or cleaves with significantly less efficiency, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, e.g., as measured by an assay described herein. The reference Cas9 molecule can by a naturally occurring unmodified Cas9 molecule, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S. pyogenes, or S. thermophilus. In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology.

In an embodiment, an eaCas9 molecule or eaCas9 polypeptide comprises an inactive, or cleavage incompetent, HNH domain and an active, or cleavage competent, N-terminal RuvC-like domain (e.g., an N-terminal RuvC-like domain described herein, e.g., SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, or SEQ ID NO: 16). Exemplary inactive, or cleavage incompetent HNH-like domains can have a mutation at one or more of: a histidine in an HNH-like domain, e.g., a histidine shown at position 856 of FIGS. 2A-2G, e.g., can be substituted with an alanine; and one or more asparagines in an HNH-like domain, e.g., an asparagine shown at position 870 of FIGS. 2A-2G and/or at position 879 of FIGS. 2A-2G, e.g., can be substituted with an alanine. In an embodiment, the eaCas9 differs from wild type in the HNH-like domain and does not cleave the target nucleic acid, or cleaves with significantly less efficiency, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, e.g., as measured by an assay described herein. The reference Cas9 molecule can by a naturally occurring unmodified Cas9 molecule, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S. pyogenes, or S. thermophilus. In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology.

Alterations in the Ability to Cleave One or Both Strands of a Target Nucleic Acid

In an embodiment, exemplary Cas9 activities comprise one or more of PAM specificity, cleavage activity, and helicase activity. A mutation(s) can be present, e.g., in one or more RuvC-like domain, e.g., an N-terminal RuvC-like domain; an HNH-like domain; a region outside the RuvC-like domains and the HNH-like domain. In some embodiments, a mutation(s) is present in a RuvC-like domain, e.g., an N-terminal RuvC-like domain. In some embodiments, a mutation(s) is present in an HNH-like domain. In some embodiments, mutations are present in both a RuvC-like domain, e.g., an N-terminal RuvC-like domain, and an HNH-like domain.

Exemplary mutations that may be made in the RuvC domain or HNH domain with reference to the S. pyogenes sequence include: D10A, E762A, H840A, N854A, N863A and/or D986A.

In an embodiment, a Cas9 molecule or Cas9 polypeptide is an eiCas9 molecule or eiCas9 polypeptide comprising one or more differences in a RuvC domain and/or in an HNH domain as compared to a reference Cas9 molecule, and the eiCas9 molecule or eiCas9 polypeptide does not cleave a nucleic acid, or cleaves with significantly less efficiency than does wildtype, e.g., when compared with wild type in a cleavage assay, e.g., as described herein, cuts with less than 50, 25, 10, or 1% of a reference Cas9 molecule, as measured by an assay described herein.

Whether or not a particular sequence, e.g., a substitution, may affect one or more activity, such as targeting activity, cleavage activity, etc., can be evaluated or predicted, e.g., by evaluating whether the mutation is conservative or by the method described in Section V. In an embodiment, a “non-essential” amino acid residue, as used in the context of a Cas9 molecule, is a residue that can be altered from the wild-type sequence of a Cas9 molecule, e.g., a naturally occurring Cas9 molecule, e.g., an eaCas9 molecule, without abolishing or more preferably, without substantially altering a Cas9 activity (e.g., cleavage activity), whereas changing an “essential” amino acid residue results in a substantial loss of activity (e.g., cleavage activity).

In an embodiment, a Cas9 molecule or Cas9 polypeptide comprises a cleavage property that differs from naturally occurring Cas9 molecules, e.g., that differs from the naturally occurring Cas9 molecule having the closest homology. For example, a Cas9 molecule or Cas9 polypeptide can differ from naturally occurring Cas9 molecules, e.g., a Cas9 molecule of S aureus, S. pyogenes, or C. jejuni as follows: its ability to modulate, e.g., decreased or increased, cleavage of a double stranded break (endonuclease and/or exonuclease activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S aureus, S. pyogenes, or C. jejuni); its ability to modulate, e.g., decreased or increased, cleavage of a single strand of a nucleic acid, e.g., a non-complimentary strand of a nucleic acid molecule or a complementary strand of a nucleic acid molecule (nickase activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S aureus, S. pyogenes, or C. jejuni); or the ability to cleave a nucleic acid molecule, e.g., a double stranded or single stranded nucleic acid molecule, can be eliminated.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is an eaCas9 molecule or eaCas9 polypeptide comprising one or more of the following activities: cleavage activity associated with a RuvC domain; cleavage activity associated with an HNH domain; cleavage activity associated with an HNH domain and cleavage activity associated with a RuvC domain.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is an eiCas9 molecule or eiCas9 polypeptide which does not cleave a nucleic acid molecule (either double stranded or single stranded nucleic acid molecules) or cleaves a nucleic acid molecule with significantly less efficiency, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, e.g., as measured by an assay described herein. The reference Cas9 molecule can be a naturally occurring unmodified Cas9 molecule, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S. pyogenes, S. thermophilus, S. aureus, C. jejuni or N. meningitidis. In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology. In an embodiment, the eiCas9 molecule or eiCas9 polypeptide lacks substantial cleavage activity associated with a RuvC domain and cleavage activity associated with an HNH domain.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is an eaCas9 molecule or eaCas9 polypeptide comprising the fixed amino acid residues of S. pyogenes shown in the consensus sequence disclosed in FIGS. 2A-2G, and has one or more amino acids that differ from the amino acid sequence of S. pyogenes (e.g., has a substitution) at one or more residue (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) represented by an “-” in the consensus sequence disclosed in FIGS. 2A-2G or SEQ ID NO: 7.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide comprises a sequence in which:

the sequence corresponding to the fixed sequence of the consensus sequence disclosed in FIGS. 2A-2G differs at no more than 1, 2, 3, 4, 5, 10, 15, or 20% of the fixed residues in the consensus sequence disclosed in FIGS. 2A-2G;

the sequence corresponding to the residues identified by “*” in the consensus sequence disclosed in FIGS. 2A-2G differ at no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the “*” residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. pyogenes Cas9 molecule; and,

the sequence corresponding to the residues identified by “-” in the consensus sequence disclosed in FIGS. 2A-2G differ at no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 55, or 60% of the “-” residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. pyogenes Cas9 molecule.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is an eaCas9 molecule or eaCas9 polypeptide comprising the fixed amino acid residues of S. thermophilus shown in the consensus sequence disclosed in FIGS. 2A-2G, and has one or more amino acids that differ from the amino acid sequence of S. thermophilus (e.g., has a substitution) at one or more residue (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) represented by an “-” in the consensus sequence disclosed in FIGS. 2A-2G.

In an embodiment the altered Cas9 molecule or Cas9 polypeptide comprises a sequence in which:

the sequence corresponding to the fixed sequence of the consensus sequence disclosed in FIGS. 2A-2G differs at no more than 1, 2, 3, 4, 5, 10, 15, or 20% of the fixed residues in the consensus sequence disclosed in FIGS. 2A-2G;

the sequence corresponding to the residues identified by “*”in the consensus sequence disclosed in FIGS. 2A-2G differ at no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the “*” residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. thermophilus Cas9 molecule; and,

the sequence corresponding to the residues identified by “-” in the consensus sequence disclosed in FIGS. 2A-2G differ at no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 55, or 60% of the “-” residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. thermophilus Cas9 molecule.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is an eaCas9 molecule or eaCas9 polypeptide comprising the fixed amino acid residues of S. mutans shown in the consensus sequence disclosed in FIGS. 2A-2G, and has one or more amino acids that differ from the amino acid sequence of S. mutans (e.g., has a substitution) at one or more residue (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) represented by an “-” in the consensus sequence disclosed in FIGS. 2A-2G.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide comprises a sequence in which:

the sequence corresponding to the fixed sequence of the consensus sequence disclosed in FIGS. 2A-2G differs at no more than 1, 2, 3, 4, 5, 10, 15, or 20% of the fixed residues in the consensus sequence disclosed in FIGS. 2A-2G;

the sequence corresponding to the residues identified by “*” in the consensus sequence disclosed in FIGS. 2A-2G differ at no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the “*” residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. mutans Cas9 molecule; and,

the sequence corresponding to the residues identified by “-” in the consensus sequence disclosed in FIGS. 2A-2G differ at no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 55, or 60% of the “-” residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. mutans Cas9 molecule.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide is an eaCas9 molecule or eaCas9 polypeptide comprising the fixed amino acid residues of L. innocula shown in the consensus sequence disclosed in FIGS. 2A-2G, and has one or more amino acids that differ from the amino acid sequence of L. innocula (e.g., has a substitution) at one or more residue (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) represented by an “-”in the consensus sequence disclosed in FIGS. 2A-2G.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide comprises a sequence in which:

the sequence corresponding to the fixed sequence of the consensus sequence disclosed in FIGS. 2A-2G differs at no more than 1, 2, 3, 4, 5, 10, 15, or 20% of the fixed residues in the consensus sequence disclosed in FIGS. 2A-2G;

the sequence corresponding to the residues identified by “*” in the consensus sequence disclosed in FIGS. 2A-2G differ at no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the “*” residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an L. innocula Cas9 molecule; and,

the sequence corresponding to the residues identified by “-” in the consensus sequence disclosed in FIGS. 2A-2G differ at no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 55, or 60% of the “-” residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an L. innocula Cas9 molecule.

In an embodiment, the altered Cas9 molecule or Cas9 polypeptide, e.g., an eaCas9 molecule, can be a fusion, e.g., of two of more different Cas9 molecules or Cas9 polypeptides, e.g., of two or more naturally occurring Cas9 molecules of different species. For example, a fragment of a naturally occurring Cas9 molecule of one species can be fused to a fragment of a Cas9 molecule of a second species. As an example, a fragment of Cas9 molecule of S. pyogenes comprising an N-terminal RuvC-like domain can be fused to a fragment of Cas9 molecule of a species other than S. pyogenes (e.g., S. thermophilus) comprising an HNH-like domain.

Cas9 Molecules and Cas9 Polypeptides with Altered PAM Recognition or No PAM Recognition

Naturally occurring Cas9 molecules can recognize specific PAM sequences, for example, the PAM recognition sequences described above for S. pyogenes, S. thermophilus, S. mutans, S. aureus and N. meningitidis.

In an embodiment, a Cas9 molecule or Cas9 polypeptide has the same PAM specificities as a naturally occurring Cas9 molecule. In other embodiments, a Cas9 molecule or Cas9 polypeptide has a PAM specificity not associated with a naturally occurring Cas9 molecule, or a PAM specificity not associated with the naturally occurring Cas9 molecule to which it has the closest sequence homology. For example, a naturally occurring Cas9 molecule can be altered, e.g., to alter PAM recognition, e.g., to alter the PAM sequence that the Cas9 molecule recognizes to decrease off target sites and/or improve specificity; or eliminate a PAM recognition requirement. In an embodiment, a Cas9 molecule or Cas9 polypeptide can be altered, e.g., to increase length of PAM recognition sequence and/or improve Cas9 specificity to high level of identity, e.g., to decrease off target sites and increase specificity. In an embodiment, the length of the PAM recognition sequence is at least 4, 5, 6, 7, 8, 9, 10 or 15 amino acids in length. Cas9 molecules or Cas9 polypeptides that recognize different PAM sequences and/or have reduced off-target activity can be generated using directed evolution. Exemplary methods and systems that can be used for directed evolution of Cas9 molecules are described, e.g., in Esvelt 2011. Candidate Cas9 molecules can be evaluated, e.g., by methods described in Section V.

Alterations of the PI domain, which mediates PAM recognition, are discussed below.

Synthetic Cas9 Molecules and Cas9 Polypeptides with Altered PI Domains

Current genome-editing methods are limited in the diversity of target sequences that can be targeted by the PAM sequence that is recognized by the Cas9 molecule utilized. A synthetic Cas9 molecule (or Syn-Cas9 molecule), or synthetic Cas9 polypeptide (or Syn-Cas9 polypeptide), as that term is used herein, refers to a Cas9 molecule or Cas9 polypeptide that comprises a Cas9 core domain from one bacterial species and a functional altered PI domain, i.e., a PI domain other than that naturally associated with the Cas9 core domain, e.g., from a different bacterial species.

In an embodiment, the altered PI domain recognizes a PAM sequence that is different from the PAM sequence recognized by the naturally-occurring Cas9 from which the Cas9 core domain is derived. In an embodiment, the altered PI domain recognizes the same PAM sequence recognized by the naturally-occurring Cas9 from which the Cas9 core domain is derived, but with different affinity or specificity. A Syn-Cas9 molecule or Syn-Cas9 polypeptide can be, respectively, a Syn-eaCas9 molecule or Syn-eaCas9 polypeptide or a Syn-eiCas9 molecule Syn-eiCas9 polypeptide.

An exemplary Syn-Cas9 molecule or Syn-Cas9 polypeptide comprises:

a) a Cas9 core domain, e.g., a Cas9 core domain from Table 12 or 13, e.g., a S. aureus, S. pyogenes, or C. jejuni Cas9 core domain; and

b) an altered PI domain from a species X Cas9 sequence selected from Tables 15 and 16.

In an embodiment, the RKR motif (the PAM binding motif) of said altered PI domain comprises: differences at 1, 2, or 3 amino acid residues; a difference in amino acid sequence at the first, second, or third position; differences in amino acid sequence at the first and second positions, the first and third positions, or the second and third positions; as compared with the sequence of the RKR motif of the native or endogenous PI domain associated with the Cas9 core domain.

In an embodiment, the Cas9 core domain comprises the Cas9 core domain from a species X Cas9 from Table 12 and said altered PI domain comprises a PI domain from a species Y Cas9 from Table 12.

In an embodiment, the RKR motif of the species X Cas9 is other than the RKR motif of the species Y Cas9.

In an embodiment, the RKR motif of the altered PI domain is selected from XXY, XNG, and XNQ.

In an embodiment, the altered PI domain has at least 60, 70, 80, 90, 95, or 100% homology with the amino acid sequence of a naturally occurring PI domain of said species Y from Table 12.

In an embodiment, the altered PI domain differs by no more than 50, 40, 30, 25, 20, 15, 10, 5, 4, 3, 2, or 1 amino acid residue from the amino acid sequence of a naturally occurring PI domain of said second species from Table 12.

In an embodiment, the Cas9 core domain comprises a S. aureus core domain and altered PI domain comprises: an A. denitrificans PI domain; a C. jejuni PI domain; a H. mustelae PI domain; or an altered PI domain of species X PI domain, wherein species X is selected from Table 16.

In an embodiment, the Cas9 core domain comprises a S. pyogenes core domain and the altered PI domain comprises: an A. denitrificans PI domain; a C. jejuni PI domain; a H. mustelae PI domain; or an altered PI domain of species X PI domain, wherein species X is selected from Table 16.

In an embodiment, the Cas9 core domain comprises a C. jejuni core domain and the altered PI domain comprises: an A. denitrificans PI domain; a H. mustelae PI domain; or an altered PI domain of species X PI domain, wherein species X is selected from Table 16.

In an embodiment, the Cas9 molecule or Cas9 polypeptide further comprises a linker disposed between said Cas9 core domain and said altered PI domain.

In an embodiment, the linker comprises: a linker described elsewhere herein disposed between the Cas9 core domain and the heterologous PI domain. Suitable linkers are further described in Section VI.

Exemplary altered PI domains for use in Syn-Cas9 molecules are described in Tables 15 and 16. The sequences for the 83 Cas9 orthologs referenced in Tables 15 and 16 are provided in Table 12. Table 14 provides the Cas9 orthologs with known PAM sequences and the corresponding RKR motif.

In an embodiment, a Syn-Cas9 molecule or Syn-Cas9 polypeptide may also be size-optimized, e.g., the Syn-Cas9 molecule or Syn-Cas9 polypeptide comprises one or more deletions, and optionally one or more linkers disposed between the amino acid residues flanking the deletions. In an embodiment, a Syn-Cas9 molecule or Syn-Cas9 polypeptide comprises a REC deletion.

Size-Optimized Cas9 Molecules and Cas9 Polypeptides

Engineered Cas9 molecules and engineered Cas9 polypeptides described herein include a Cas9 molecule or Cas9 polypeptide comprising a deletion that reduces the size of the molecule while still retaining desired Cas9 properties, e.g., essentially native conformation, Cas9 nuclease activity, and/or target nucleic acid molecule recognition. Provided herein are Cas9 molecules or Cas9 polypeptides comprising one or more deletions and optionally one or more linkers, wherein a linker is disposed between the amino acid residues that flank the deletion. Methods for identifying suitable deletions in a reference Cas9 molecule, methods for generating Cas9 molecules with a deletion and a linker, and methods for using such Cas9 molecules will be apparent to one of ordinary skill in the art upon review of this document.

A Cas9 molecule, e.g., a S. aureus, S. pyogenes, or C. jejuni, Cas9 molecule, having a deletion is smaller, e.g., has reduced number of amino acids, than the corresponding naturally-occurring Cas9 molecule. The smaller size of the Cas9 molecules allows increased flexibility for delivery methods, and thereby increases utility for genome-editing. A Cas9 molecule or Cas9 polypeptide can comprise one or more deletions that do not substantially affect or decrease the activity of the resultant Cas9 molecules or Cas9 polypeptides described herein. Activities that are retained in the Cas9 molecules or Cas9 polypeptides comprising a deletion as described herein include one or more of the following:

a nickase activity, i.e., the ability to cleave a single strand, e.g., the non-complementary strand or the complementary strand, of a nucleic acid molecule; a double stranded nuclease activity, i.e., the ability to cleave both strands of a double stranded nucleic acid and create a double stranded break, which in an embodiment is the presence of two nickase activities;

an endonuclease activity;

an exonuclease activity;

a helicase activity, i.e., the ability to unwind the helical structure of a double stranded nucleic acid;

and recognition activity of a nucleic acid molecule, e.g., a target nucleic acid or a gRNA.

Activity of the Cas9 molecules or Cas9 polypeptides described herein can be assessed using the activity assays described herein or in the art.

Identifying Regions Suitable for Deletion

Suitable regions of Cas9 molecules for deletion can be identified by a variety of methods. Naturally-occurring orthologous Cas9 molecules from various bacterial species, e.g., any one of those listed in Table 12, can be modeled onto the crystal structure of S. pyogenes Cas9 (Nishimasu 2014) to examine the level of conservation across the selected Cas9 orthologs with respect to the three-dimensional conformation of the protein. Less conserved or unconserved regions that are spatially located distant from regions involved in Cas9 activity, e.g., interface with the target nucleic acid molecule and/or gRNA, represent regions or domains are candidates for deletion without substantially affecting or decreasing Cas9 activity.

REC-Optimized Cas9 Molecules and Cas9 Polypeptides

A REC-optimized Cas9 molecule, or a REC-optimized Cas9 polypeptide, as that term is used herein, refers to a Cas9 molecule or Cas9 polypeptide that comprises a deletion in one or both of the REC2 domain and the RE1c_(T) domain (collectively a REC deletion), wherein the deletion comprises at least 10% of the amino acid residues in the cognate domain. A REC-optimized Cas9 molecule or Cas9 polypeptide can be an eaCas9 molecule or eaCas9 polypeptide, or an eiCas9 molecule or eiCas9 polypeptide. An exemplary REC-optimized Cas9 molecule or REC-optimized Cas9 polypeptide comprises:

a) a deletion selected from:

-   -   i) a REC2 deletion;     -   ii) a REC1_(CT) deletion; or     -   iii) a REC1_(SUB) deletion.

Optionally, a linker is disposed between the amino acid residues that flank the deletion. In an embodiment, a Cas9 molecule or Cas9 polypeptide includes only one deletion, or only two deletions. A Cas9 molecule or Cas9 polypeptide can comprise a REC2 deletion and a REC1_(CT) deletion. A Cas9 molecule or Cas9 polypeptide can comprise a REC2 deletion and a REC1_(SUB) deletion.

Generally, the deletion will contain at least 10% of the amino acids in the cognate domain, e.g., a REC2 deletion will include at least 10% of the amino acids in the REC2 domain.

A deletion can comprise: at least 10, 20, 30, 40, 50, 60, 70, 80, or 90% of the amino acid residues of its cognate domain; all of the amino acid residues of its cognate domain; an amino acid residue outside its cognate domain; a plurality of amino acid residues outside its cognate domain; the amino acid residue immediately N terminal to its cognate domain; the amino acid residue immediately C terminal to its cognate domain; the amino acid residue immediately N terminal to its cognate and the amino acid residue immediately C terminal to its cognate domain; a plurality of, e.g., up to 5, 10, 15, or 20, amino acid residues N terminal to its cognate domain; a plurality of, e.g., up to 5, 10, 15, or 20, amino acid residues C terminal to its cognate domain; a plurality of, e.g., up to 5, 10, 15, or 20, amino acid residues N terminal to its cognate domain and a plurality of e.g., up to 5, 10, 15, or 20, amino acid residues C terminal to its cognate domain.

In an embodiment, a deletion does not extend beyond: its cognate domain; the N terminal amino acid residue of its cognate domain; the C terminal amino acid residue of its cognate domain.

A REC-optimized Cas9 molecule or REC-optimized Cas9 polypeptide can include a linker disposed between the amino acid residues that flank the deletion. Suitable linkers for use between the amino acid resides that flank a REC deletion in a REC-optimized Cas9 molecule or REC-optimized Cas9 polypeptide is disclosed in Section VI.

In an embodiment, a REC-optimized Cas9 molecule or REC-optimized Cas9 polypeptide comprises an amino acid sequence that, other than any REC deletion and associated linker, has at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 99, or 100% homology with the amino acid sequence of a naturally occurring Cas 9, e.g., a Cas9 molecule described in Table 12, e.g., a S. aureus Cas9 molecule, a S. pyogenes Cas9 molecule, or a C. jejuni Cas9 molecule.

In an embodiment, a REC-optimized Cas9 molecule or REC-optimized Cas9 polypeptide comprises an amino acid sequence that, other than any REC deletion and associated linker, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25, amino acid residues from the amino acid sequence of a naturally occurring Cas 9, e.g., a Cas9 molecule described in Table 12, e.g., a S. aureus Cas9 molecule, a S. pyogenes Cas9 molecule, or a C. jejuni Cas9 molecule.

In an embodiment, a REC-optimized Cas9 molecule or REC-optimized Cas9 polypeptide comprises an amino acid sequence that, other than any REC deletion and associate linker, differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25% of the, amino acid residues from the amino acid sequence of a naturally occurring Cas 9, e.g., a Cas9 molecule described in Table 12, e.g., a S. aureus Cas9 molecule, a S. pyogenes Cas9 molecule, or a C. jejuni Cas9 molecule.

For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. Methods of alignment of sequences for comparison are well known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman 1981, by the homology alignment algorithm of Needleman & Wunsch 1970, by the search for similarity method of Pearson & Lipman 1988, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Brent et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (2003)).

Two examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul 1977 and Altschul 1990), respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.

The percent identity between two amino acid sequences can also be determined using the algorithm of Myers 1988, which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. In addition, the percent identity between two amino acid sequences can be determined using the Needleman & Wunsch 1970 algorithm, which has been incorporated into the GAP program in the GCG software package (available at www.gcg.com), using either a Blossom 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.

Sequence information for exemplary REC deletions are provided for 83 naturally-occurring Cas9 orthologs in Table 12. The amino acid sequences of exemplary Cas9 molecules from different bacterial species are shown below.

TABLE 12 Amino Acid Sequence of Cas9 Orthologs REC2 REC1_(CT) Rec_(sub) Amino start stop start stop start stop acid (AA (AA # AA (AA (AA # AA (AA (AA # AA Species/Composite ID sequence pos) pos) deleted pos) pos) deleted pos) pos) deleted Staphylococcus aureus SEQ ID 126 166 41 296 352 57 296 352 57 tr|J7RUA5|J7RUA5_STAAU NO: 26 Streptococcus pyogenes SEQ ID 176 314 139 511 592 82 511 592 82 sp|Q99ZW2|CAS9_STRP1 NO: 2 Campylobacter jejuni NCTC 11168 SEQ ID 137 181 45 316 360 45 316 360 45 gi|218563121|ref|YP_002344900.1 NO: 306 Bacteroides fragilis NCTC 9343 SEQ ID 148 339 192 524 617 84 524 617 84 gi|60683389|ref|YP_213533.1| NO: 307 Bifidobacterium bifidum S17 SEQ ID 173 335 163 516 607 87 516 607 87 gi|310286728|ref|YP_003937986. NO: 308 Veillonella atypica ACS-134-V-Col7a SEQ ID 185 339 155 574 663 79 574 663 79 gi|303229466|ref|ZP_07316256.1 NO: 309 Lactobacillus rhamnosus GG SEQ ID 169 320 152 559 645 78 559 645 78 gi|258509199|ref|YP_003171950.1 NO: 310 Filifactor alocis ATCC 35896 SEQ ID 166 314 149 508 592 76 508 592 76 gi|374307738|ref|YP_005054169.1 NO: 311 Oenococcus kitaharae DSM 17330 SEQ ID 169 317 149 555 639 80 555 639 80 gi|366983953|gb|EHN59352.1| NO: 312 Fructobacillus fructosus KCTC 3544 SEQ ID 168 314 147 488 571 76 488 571 76 gi|339625081|ref|ZP_08660870.1 NO: 313 Catenibacterium mitsuokai DSM 15897 SEQ ID 173 318 146 511 594 78 511 594 78 gi|224543312|ref|ZP_03683851.1 NO: 314 Finegoldia magna ATCC 29328 SEQ ID 168 313 146 452 534 77 452 534 77 gi|169823755|ref|YP_001691366.1 NO: 315 Coriobacterium glomerans PW2 SEQ ID 175 318 144 511 592 82 511 592 82 gi|328956315|ref|YP_004373648.1 NO: 316 Eubacterium yurii ATCC 43715 SEQ ID 169 310 142 552 633 76 552 633 76 gi|306821691|ref|ZP_07455288.1 NO: 317 Peptoniphilus duerdenii SEQ ID 171 311 141 535 615 76 535 615 76 ATCC BAA-1640 NO: 318 gi|304438954|ref|ZP_07398877.1 Acidaminococcus sp. D21 SEQ ID 167 306 140 511 591 75 511 591 75 gi|227824983|ref|ZP_03989815.1 NO: 319 Lactobacillus farciminis KCTC 3681 SEQ ID 171 310 140 542 621 85 542 621 85 gi|336394882|ref|ZP_08576281.1 NO: 320 Streptococcus sanguinis SK49 SEQ ID 185 324 140 411 490 85 411 490 85 gi|422884106|ref|ZP_16930555.1 NO: 321 Coprococcus catus GD-7 SEQ ID 172 310 139 556 634 76 556 634 76 gi|291520705|emb|CBK78998.1| NO: 322 Streptococcus mutans UA159 SEQ ID 176 314 139 392 470 84 392 470 84 gi|24379809|ref|NP_721764.1| NO: 1 Streptococcus pyogenes M1 GAS SEQ ID 176 314 139 523 600 82 523 600 82 gi|13622193|gb|AAK33936.1| NO: 2 Streptococcus thermophilus LMD-9 SEQ ID 176 314 139 481 558 81 481 558 81 gi|116628213|ref|YP_820832.1| NO: 3 Fusobacterium nucleatum ATCC 49256 SEQ ID 171 308 138 537 614 76 537 614 76 gi|34762592|ref|ZP_00143587.1| NO: 326 Planococcus antarcticus DSM 14505 SEQ ID 162 299 138 538 614 94 538 614 94 gi|389815359|ref|ZP_10206685.1 NO: 327 Treponema denticola ATCC 35405 SEQ ID 169 305 137 524 600 81 524 600 81 gi|42525843|ref|NP_970941.1| NO: 328 Solobacterium moorei F0204 SEQ ID 179 314 136 544 619 77 544 619 77 gi|320528778|ref|ZP_08029929.1 NO: 329 Staphylococcus pseudintermedius ED99 SEQ ID 164 299 136 531 606 92 531 606 92 gi|323463801|gb|ADX75954.1| NO: 330 Flavobacterium branchiophilum FL-15 SEQ ID 162 286 125 538 613 63 538 613 63 gi|347536497|ref|YP_004843922.1 NO: 331 Ignavibacterium album JCM 16511 SEQ ID 223 329 107 357 432 90 357 432 90 gi|385811609|ref|YP_005848005.1 NO: 332 Bergeyella zoohelcum ATCC 43767 SEQ ID 165 261 97 529 604 56 529 604 56 gi|423317190|ref|ZP_17295095.1 NO: 333 Nitrobacter hamburgensis X14 SEQ ID 169 253 85 536 611 48 536 611 48 gi|92109262|ref|YP_571550.1| NO: 334 Odoribacter laneus YIT 12061 SEQ ID 164 242 79 535 610 63 535 610 63 gi|374384763|ref|ZP_09642280.1 NO: 335 Legionella pneumophila str. Paris SEQ ID 164 239 76 402 476 67 402 476 67 gi|54296138|ref|YP_122507.1| NO: 336 Bacteroides sp. 20_3 SEQ ID 198 269 72 530 604 83 530 604 83 gi|301311869|ref|ZP_07217791.1 NO: 337 Akkermansia muciniphila SEQ ID 136 202 67 348 418 62 348 418 62 ATCC BAA-835 NO: 338 gi|187736489|ref|YP_001878601. Prevotella sp. C561 SEQ ID 184 250 67 357 425 78 357 425 78 gi|345885718|ref|ZP_08837074.1 NO: 339 Wolinella succinogenes DSM 1740 SEQ ID 157 218 36 401 468 60 401 468 60 gi|34557932|ref|NP_907747.1| NO: 340 Alicyclobacillus hesperidum SEQ ID 142 196 55 416 482 61 416 482 61 URH17-3-68 NO: 341 gi|403744858|ref|ZP_10953934.1 Caenispirillum salinarum AK4 SEQ ID 161 214 54 330 393 68 330 393 68 gi|427429481|ref|ZP_18919511.1 NO: 342 Eubacterium rectale ATCC 33656 SEQ ID 133 185 53 322 384 60 322 384 60 gi|238924075|ref|YP_002937591.1 NO: 343 Mycoplasma synoviae 53 SEQ ID 187 239 53 319 381 80 319 381 80 gi|71894592|ref|YP_278700.1| NO: 344 Porphyromonas SEQ ID 150 202 53 309 371 60 309 371 60 sp. oral taxon 279 str. F0450 NO: 345 gi|402847315|ref|ZP_10895610.1 Streptococcus thermophilus LMD-9 SEQ ID 127 178 139 424 486 81 424 486 81 gi|116627542|ref|YP_820161.1| NO: 346 Roseburia inulinivorans DSM 16841 SEQ ID 154 204 51 318 380 69 318 380 69 gi|225377804|ref|ZP_03755025.1 NO: 347 Methylosinus trichosporium OB3b SEQ ID 144 193 50 426 488 64 426 488 64 gi|296446027|ref|ZP_06887976.1 NO: 348 Ruminococcus albus 8 SEQ ID 139 187 49 351 412 55 351 412 55 gi|325677756|ref|ZP_08157403.1 NO: 349 Bifidobacterium longum DJO10A SEQ ID 183 230 48 370 431 44 370 431 44 gi|189440764|ref|YP_001955845. NO: 350 Enterococcus faecalis TX0012 SEQ ID 123 170 48 327 387 60 327 387 60 gi|315149830|gb|EFT93846.1| NO: 351 Mycoplasma mobile 163K SEQ ID 179 226 48 314 374 79 314 374 79 gi|47458868|ref|YP_015730.1| NO: 352 Actinomyces coleocanis DSM 15436 SEQ ID 147 193 47 358 418 40 358 418 40 gi|227494853|ref|ZP_03925169.1 NO: 353 Dinoroseobacter shibae DFL 12 SEQ ID 138 184 47 338 398 48 338 398 48 gi|159042956|ref|YP_001531750.1 NO: 354 Actinomyces SEQ ID 183 228 46 349 409 40 349 409 40 sp. oral taxon 180 str. F0310 NO: 355 gi|315605738|ref|ZP_07880770.1 Alcanivorax sp. W11-5 SEQ ID 139 183 45 344 404 61 344 404 61 gi|407803669|ref|ZP_11150502.1 NO: 356 Aminomonas paucivorans DSM 12260 SEQ ID 134 178 45 341 401 63 341 401 63 gi|312879015|ref|ZP_07738815.1 NO: 357 Mycoplasma canis PG 14 SEQ ID 139 183 45 319 379 76 319 379 76 gi|384393286|gb|EIE39736.1| NO: 358 Lactobacillus coryniformis KCTC 3535 SEQ ID 141 184 44 328 387 61 328 387 61 gi|336393381|ref|ZP_08574780.1 NO: 359 Elusimicrobium minutum Pei191 SEQ ID 177 219 43 322 381 47 322 381 47 gi|187250660|ref|YP_001875142.1 NO: 360 Neisseria meningitidis Z2491 SEQ ID 147 189 43 360 419 61 360 419 61 gi|218767588|ref|YP_002342100.1 NO: 25 Pasteurella multocida str. Pm70 SEQ ID 139 181 43 319 378 61 319 378 61 gi|15602992|ref|NP_246064.1| NO: 362 Rhodovulum sp. PH10 SEQ ID 141 183 43 319 378 48 319 378 48 gi|402849997|ref|ZP_10898214.1 NO: 363 Eubacterium dolichum DSM 3991 SEQ ID 131 172 42 303 361 59 303 361 59 gi|160915782|ref|ZP_02077990.1 NO: 364 Nitratifractor salsuginis DSM 16511 SEQ ID 143 184 42 347 404 61 347 404 61 gi|319957206|ref|YP_004168469.1 NO: 365 Rhodospirillum rubrum ATCC 11170 SEQ ID 139 180 42 314 371 55 314 371 55 gi|83591793|ref|YP_425545.1| NO: 366 Clostridium cellulolyticum H10 SEQ ID 137 176 40 320 376 61 320 376 61 gi|220930482|ref|YP_002507391.1 NO: 367 Helicobacter mustelae 12198 SEQ ID 148 187 40 298 354 48 298 354 48 gi|291276265|ref|YP_003516037.1 NO: 368 Ilyobacter polytropus DSM 2926 SEQ ID 134 173 40 462 517 63 462 517 63 gi|310780384|ref|YP_003968716.1 NO: 369 Sphaerochaeta globus str. Buddy SEQ ID 163 202 40 335 389 45 335 389 45 gi|325972003|ref|YP_004248194.1 NO: 370 Staphylococcus lugdunensis M23590 SEQ ID 128 167 40 337 391 57 337 391 57 gi|315659848|ref|ZP_07912707.1 NO: 371 Treponema sp. JC4 SEQ ID 144 183 40 328 382 63 328 382 63 gi|384109266|ref|ZP_10010146.1 NO: 372 Uncultured Deltaproteobacterium SEQ ID 154 193 40 313 365 55 313 365 55 HF0070 07E19 NO: 373 gi|297182908|gb|ADI19058.1| Alicycliphilus denitrificans K601 SEQ ID 140 178 39 317 366 48 317 366 48 gi|330822845|ref|YP_004386148.1 NO: 374 Azospirillum sp. B510 SEQ ID 205 243 39 342 389 46 342 389 46 gi|288957741|ref|YP_003448082.1 NO: 375 Bradyrhizobium sp. BTAi1 SEQ ID 143 181 39 323 370 48 323 370 48 gi|148255343|ref|YP_001239928.1 NO: 376 Parvibaculum lavamentivorans DS-1 SEQ ID 138 176 39 327 374 58 327 374 58 gi|154250555|ref|YP_001411379.1 NO: 377 Prevotella timonensis CRIS 5C-B1 SEQ ID 170 208 39 328 375 61 328 375 61 gi|282880052|ref|ZP_06288774.1 NO: 378 Bacillus smithii 7 3 47FAA SEQ ID 134 171 38 401 448 63 401 448 63 gi|365156657|ref|ZP_09352959.1 NO: 379 Candidatus Puniceispirillum SEQ ID 135 172 38 344 391 53 344 391 53 marinum IMCC1322 NO: 380 gi|294086111|ref|YP_003552871.1 Barnesiella intestinihominis YIT 11860 SEQ ID 140 176 37 371 417 60 371 417 60 gi|404487228|ref|ZP_11022414.1 NO: 381 Ralstonia syzygii R24 SEQ ID 140 176 37 395 440 50 395 440 50 gi|344171927|emb|CCA84553.1| NO: 382 Wolinella succinogenes DSM 1740 SEQ ID 145 180 36 348 392 60 348 392 60 gi|34557790|ref|NP_907605.1| NO: 383 Mycoplasma gallisepticum str. F SEQ ID 144 177 34 373 416 71 373 416 71 gi|284931710|gb|ADC31648.1| NO: 384 Acidothermus cellulolyticus 11B SEQ ID 150 182 33 341 380 58 341 380 58 gi|117929158|ref|YP_873709.1| NO: 385 Mycoplasma ovipneumoniae SC01 SEQ ID 156 184 29 381 420 62 381 420 62 gi|363542550|ref|ZP_09312133.1 NO: 386

TABLE 13 Amino Acid Sequence of Cas9 Core Domains Cas9 Start Cas9 Stop (AA pos) (AA pos) Start and Stop numbers refer Strain Name to the sequence in Table 11 Staphylococcus aureus 1 772 Streptococcus pyogenes 1 1099 Campulobacter jejuni 1 741

TABLE 14 Identified PAM sequences and corresponding RKR motifs. RKR PAM sequence motif Strain Name (NA) (AA) Streptococcus pyogenes NGG RKR Streptococcus mutans NGG RKR Streptococcus thermophilus NGGNG RYR A Treponema denticola NAAAAN VAK Streptococcus thermophilus NNAAAAW IYK B Campylobacter jejuni NNNNACA NLK Pasteurella multocida GNNNCNNA KDG Neisseria meningitidis NNNNGATT or IGK Staphylococcus aureus NNGRRV (R = A or G; NDK V = A. G or C) NNGRRT (R = A or G) PI domains are provided in Tables 15 and 16.

TABLE 15 Altered PI Domains PI Start PI Stop (AA pos) (AA pos) Length RKR Start and Stop numbers refer of PI motif Strain Name to the sequences in Table 11 (AA) (AA) Alicycliphilus denitrificans K601 837 1029 193 --Y Campylobacter jejuni NCTC 11168 741 984 244 -NG Helicobacter mustelae 12198 771 1024 254 -NQ

TABLE 16 Other Altered PI Domains PI Start PI Stop (AA pos) (AA pos) Length RKR Start and Stop numbers refer of PI motif Strain Name to the sequences in Table 11 (AA) (AA) Akkermansia muciniphila ATCC 871 1101 231 ALK BAA-835 Ralstonia syzygii R24 821 1062 242 APY Cand. Puniceispirillum marinum 815 1035 221 AYK IMCC1322 Fructobacillus fructosus KCTC 3544 1074 1323 250 DGN Eubacterium yurii ATCC 43715 1107 1391 285 DGY Eubacterium dolichum DSM 3991 779 1096 318 DKK Dinoroseobacter shibae DFL 12 851 1079 229 DPI Clostridium cellulolyticum H10 767 1021 255 EGK Pasteurella multocida str. Pm70 815 1056 242 ENN Mycoplasma canis PG 14 907 1233 327 EPK Porphyromonas sp. oral taxon 279 str. 935 1197 263 EPT F0450 Filifactor alocis ATCC 35896 1094 1365 272 EVD Aminomonas paucivorans DSM 12260 801 1052 252 EVY Wolinella succinogenes DSM 1740 1034 1409 376 EYK Oenococcus kitaharae DSM 17330 1119 1389 271 GAL CoriobacteriumglomeransPW2 1126 1384 259 GDR Peptoniphilus duerdenii ATCC 1091 1364 274 GDS BAA-1640 Bifidobacterium bifidum S17 1138 1420 283 GGL Alicyclobacillus hesperidum 876 1146 271 GGR URH17-3-68 Roseburia inulinivorans DSM 16841 895 1152 258 GGT Actinomyces coleocanis DSM 15436 843 1105 263 GKK Odoribacter laneus YIT 12061 1103 1498 396 GKV Coprococcus catus GD-7 1063 1338 276 GNQ Enterococcus faecalis TX0012 829 1150 322 GRK Bacillus smithii 7 3 47FAA 809 1088 280 GSK Legionella pneumophila str. Paris 1021 1372 352 GTM Bacteroides fragilis NCTC 9343 1140 1436 297 IPV Mycoplasma ovipneumoniae SC01 923 1265 343 IRI Actinomyces sp. oral taxon 180 str. 895 1181 287 KEK F0310 Treponema sp. JC4 832 1062 231 KIS Fusobacteriumnucleatum ATCC49256 1073 1374 302 KKV Lactobacillus farciminis KCTC 3681 1101 1356 256 KKV Nitratifractor salsuginis 840 1132 293 KMR DSM 16511 Lactobacillus coryniformis KCTC 3535 850 1119 270 KNK Mycoplasma mobile 163K 916 1236 321 KNY Flavobacterium branchiophilum FL-15 1182 1473 292 KQK Prevotella timonensis CRIS 5C-B1 957 1218 262 KQQ Methylosinus trichosporium OB3b 830 1082 253 KRP Prevotella sp. C561 1099 1424 326 KRY Mycoplasma gallisepticum str. F 911 1269 359 KTA Lactobacillus rhamnosus GG 1077 1363 287 KYG Wolinella succinogenes DSM 1740 811 1059 249 LPN Streptococcus thermophilus LMD-9 1099 1388 290 MLA Treponema denticola ATCC 35405 1092 1395 304 NDS Bergeyella zoohelcum ATCC 43767 1098 1415 318 NEK Veillonella atypica ACS-134-V-Col7a 1107 1398 292 NGF Neisseria meningitidis Z2491 835 1082 248 NHN Ignavibacterium album JCM 16511 1296 1688 393 NKK Ruminococcus albus 8 853 1156 304 NNF Streptococcus thermophilus LMD-9 811 1121 311 NNK Barnesiella intestinihominis YIT 871 1153 283 NPV 11860 Azospirillum sp. B510 911 1168 258 PFH Rhodospirillum rubrum ATCC 11170 863 1173 311 PRG Planococcus antarcticus DSM 14505 1087 1333 247 PYY Staphylococcus pseudintermedius 1073 1334 262 QIV ED99 Alcanivorax sp. W11-5 843 1113 271 RIE Bradyrhizobium sp. BTAi1 811 1064 254 RIY Streptococcus pyogenes M1 GAS 1099 1368 270 RKR Streptococcus mutans UA159 1078 1345 268 RKR Streptococcus Pyogenes 1099 1368 270 RKR Bacteroides sp. 20 3 1147 1517 371 RNI S. aureus 772 1053 282 RNK Solobacterium moorei F0204 1062 1327 266 RSG Finegoldia magna ATCC 29328 1081 1348 268 RTE uncultured delta proteobacterium 770 1011 242 SGG HF0070 07E19 Acidaminococcus sp. D21 1064 1358 295 SIG Eubacterium rectale ATCC 33656 824 1114 291 SKK Caenispirillum salinarum AK4 1048 1442 395 SLV Acidothermus cellulolyticus 11B 830 1138 309 SPS Catenibacterium mitsuokai DSM 15897 1068 1329 262 SPT Parvibaculum lavamentivorans DS-1 827 1037 211 TGN Staphylococcus lugdunensis 772 1054 283 TKK M23590 Streptococcus sanguinis SK49 1123 1421 299 TRM Elusimicrobium minutum Pei191 910 1195 286 TTG Nitrobacter hamburgensis X14 914 1166 253 VAY Mycoplasma synoviae 53 991 1314 324 VGF Sphaerochaeta globus str. Buddy 877 1179 303 VKG Ilyobacter polytropus DSM 2926 837 1092 256 VNG Rhodovulum sp. PH10 821 1059 239 VPY Bifidobacterium longum DJO10A 904 1187 284 VRK

Nucleic Acids Encoding Cas9 Molecules

Nucleic acids encoding the Cas9 molecules or Cas9 polypeptides, e.g., an eaCas9 molecule or eaCas9 polypeptide, are provided herein.

Exemplary nucleic acids encoding Cas9 molecules or Cas9 polypeptides are described in Cong 2013; Wang 2013; Mali 2013; and Jinek 2012. Another exemplary nucleic acid encoding a Cas9 molecule or Cas9 polypeptide is shown in black in FIG. 8.

In an embodiment, a nucleic acid encoding a Cas9 molecule or Cas9 polypeptide can be a synthetic nucleic acid sequence. For example, the synthetic nucleic acid molecule can be chemically modified, e.g., as described in Section VIII. In an embodiment, the Cas9 mRNA has one or more (e.g., all of the following properties: it is capped, polyadenylated, substituted with 5-methylcytidine and/or pseudouridine.

In addition, or alternatively, the synthetic nucleic acid sequence can be codon optimized, e.g., at least one non-common codon or less-common codon has been replaced by a common codon. For example, the synthetic nucleic acid can direct the synthesis of an optimized messenger mRNA, e.g., optimized for expression in a mammalian expression system, e.g., described herein.

In addition, or alternatively, a nucleic acid encoding a Cas9 molecule or Cas9 polypeptide may comprise a nuclear localization sequence (NLS). Nuclear localization sequences are known in the art.

An exemplary codon optimized nucleic acid sequence encoding a Cas9 molecule of S. pyogenes is set forth in SEQ ID NO: 22. The corresponding amino acid sequence is set forth in SEQ ID NO: 2.

An exemplary codon optimized nucleic acid sequence encoding a Cas9 molecule of N. meningitidis is set forth in SEQ ID NO: 24. The corresponding amino acid sequence is set forth in SEQ ID NO: 25.

An amino acid sequence of a S. aureus Cas9 molecule is set forth in SEQ ID NO: 26. An exemplary codon optimized nucleic acid sequence encoding a Cas9 molecule of S. aureus is set forth in SEQ ID NO: 39.

If any of the above Cas9 sequences are fused with a peptide or polypeptide at the C-terminus, it is understood that the stop codon will be removed.

Other Cas Molecules and Cas Polypeptides

Various types of Cas molecules or Cas polypeptides can be used to practice the inventions disclosed herein. In some embodiments, Cas molecules of Type II Cas systems are used. In other embodiments, Cas molecules of other Cas systems are used. For example, Type I or Type III Cas molecules may be used. Exemplary Cas molecules (and Cas systems) are described, e.g., in Haft 2005 and Makarova 2011, the contents of both references are incorporated herein by reference in their entirety. Exemplary Cas molecules (and Cas systems) are also shown in Table 17.

TABLE 17 Cas Systems Structure Families (and System of encoded superfamily) Gene type or Name from protein (PDB of encoded name^(‡) subtype Haft 2005^(§) accessions)^(¶) protein^(#)** Representatives cas1 Type I cas1 3GOD, COG1518 SERP2463, Type II 3LFX and SPy1047 and Type III 2YZS ygbT cas2 Type I cas2 2IVY, 2I8E COG1343 and SERP2462, Type II and 3EXC COG3512 SPy1048, Type III SPy1723 (N- terminal domain) and ygbF cas3′ Type I^(‡‡) cas3 NA COG1203 APE1232 and ygcB cas3″ Subtype NA NA COG2254 APE1231 and I-A BH0336 Subtype I-B cas4 Subtype cas4 and NA COG1468 APE1239 and I-A csa1 BH0340 Subtype I-B Subtype I-C Subtype I-D Subtype II-B cas5 Subtype cas5a, 3KG4 COG1688 APE1234, I-A cas5d, (RAMP) BH0337, devS Subtype cas5e, and ygcI I-B cas5h, Subtype cas5p, cas5t I-C and cmx5 Subtype I-E cas6 Subtype cas6 and 3I4H COG1583 and PF1131 and I-A cmx6 COG5551 slr7014 Subtype (RAMP) I-B Subtype I-D Subtype III-A Subtype III-B cas6e Subtype cse3 1WJ9 (RAMP) ygcH I-E cas6f Subtype csy4 2XLJ (RAMP) y1727 I-F cas7 Subtype csa2, csd2, NA COG1857 and devR and ygcJ I-A cse4, csh2, COG3649 Subtype csp1 and (RAMP) I-B cst2 Subtype I-C Subtype I-E cas8a1 Subtype cmx1, cst1, NA BH0338-like LA3191^(§§) and I-A^(‡‡) csx8, csx13 PG2018^(§§) and CXXC- CXXC cas8a2 Subtype csa4 and NA PH0918 AF0070, AF1873, I-A^(‡‡) csx9 MJ0385, PF0637, PH0918 and SSO1401 cas8b Subtype csh1 and NA BH0338-like MTH1090 and I-B^(‡‡) TM1802 TM1802 cas8c Subtype csd1 and NA BH0338-like BH0338 I-C^(‡‡) csp2 cas9 Type II^(‡‡) csn1 and NA COG3513 FTN_0757 and csx12 SPy1046 cas10 Type III^(‡‡) cmr2, csm1 NA COG1353 MTH326, and csx11 Rv2823c^(§§) and TM1794^(§§) cas10d Subtype csc3 NA COG1353 slr7011 I-D^(‡‡) csy1 Subtype csy1 NA y1724-like y1724 I-F^(‡‡) csy2 Subtype csy2 NA (RAMP) y1725 I-F csy3 Subtype csy3 NA (RAMP) y1726 I-F cse1 Subtype cse1 NA YgcL-like ygcL I-E^(‡‡) cse2 Subtype cse2 2ZCA YgcK-like ygcK I-E csc1 Subtype csc1 NA alr1563-like alr1563 I-D (RAMP) csc2 Subtype csc1 and NA COG1337 slr7012 I-D csc2 (RAMP) csa5 Subtype csa5 NA AF1870 AF1870, MJ0380, I-A PF0643 and SSO1398 csn2 Subtype csn2 NA SPy1049-like SPy1049 II-A csm2 Subtype csm2 NA COG1421 MTH1081 and III-A^(‡‡) SERP2460 csm3 Subtype csc2 and NA COG1337 MTH1080 and III-A csm3 (RAMP) SERP2459 csm4 Subtype csm4 NA COG1567 MTH1079 and III-A (RAMP) SERP2458 csm5 Subtype csm5 NA COG1332 MTH1078 and III-A (RAMP) SERP2457 csm6 Subtype APE2256 2WTE COG1517 APE2256 and III-A and csm6 SSO1445 cmr1 Subtype cmr1 NA COG1367 PF1130 III-B (RAMP) cmr3 Subtype cmr3 NA COG1769 PF1128 III-B (RAMP) cmr4 Subtype cmr4 NA COG1336 PF1126 III-B (RAMP) cmr5 Subtype cmr5 2ZOP and COG3337 MTH324 and III-B^(‡‡) 2OEB PF1125 cmr6 Subtype cmr6 NA COG1604 PF1124 III-B (RAMP) csb1 Subtype GSU0053 NA (RAMP) Balac_1306 and I-U GSU0053 csb2 Subtype NA NA (RAMP) Balac_1305 and I-U^(§§) GSU0054 csb3 Subtype NA NA (RAMP) Balac_1303^(§§) I-U csx17 Subtype NA NA NA Btus_2683 I-U csx14 Subtype NA NA NA GSU0052 I-U csx10 Subtype csx10 NA (RAMP) Caur_2274 I-U csx16 Subtype VVA1548 NA NA VVA1548 III-U csaX Subtype csaX NA NA SSO1438 III-U csx3 Subtype csx3 NA NA AF1864 III-U csx1 Subtype csa3, csx1, 1XMX and COG1517 and MJ1666, III-U csx2, 2I71 COG4006 NE0113, PF1127 DXTHG, and TM1812 NE0113 and TIGR02710 csx15 Unknown NA NA TTE2665 TTE2665 csf1 Type U csf1 NA NA AFE_1038 csf2 Type U csf2 NA (RAMP) AFE_1039 csf3 Type U csf3 NA (RAMP) AFE_1040 csf4 Type U csf4 NA NA AFE_1037

V. Functional Analysis of Candidate Molecules

Candidate Cas9 molecules, candidate gRNA molecules, candidate Cas9 molecule/gRNA molecule complexes, can be evaluated by art-known methods or as described herein. For example, exemplary methods for evaluating the endonuclease activity of Cas9 molecule are described, e.g., in Jinek 2012.

Binding and Cleavage Assay: Testing the Endonuclease Activity of Cas9 Molecule

The ability of a Cas9 molecule/gRNA molecule complex to bind to and cleave a target nucleic acid can be evaluated in a plasmid cleavage assay. In this assay, synthetic or in vitro-transcribed gRNA molecule is pre-annealed prior to the reaction by heating to 95° C. and slowly cooling down to room temperature. Native or restriction digest-linearized plasmid DNA (300 ng (˜8 nM)) is incubated for 60 min at 37° C. with purified Cas9 protein molecule (50-500 nM) and gRNA (50-500 nM, 1:1) in a Cas9 plasmid cleavage buffer (20 mM HEPES pH 7.5, 150 mM KCl, 0.5 mM DTT, 0.1 mM EDTA) with or without 10 mM MgCl₂. The reactions are stopped with 5× DNA loading buffer (30% glycerol, 1.2% SDS, 250 mM EDTA), resolved by a 0.8 or 1% agarose gel electrophoresis and visualized by ethidium bromide staining. The resulting cleavage products indicate whether the Cas9 molecule cleaves both DNA strands, or only one of the two strands. For example, linear DNA products indicate the cleavage of both DNA strands. Nicked open circular products indicate that only one of the two strands is cleaved.

Alternatively, the ability of a Cas9 molecule/gRNA molecule complex to bind to and cleave a target nucleic acid can be evaluated in an oligonucleotide DNA cleavage assay. In this assay, DNA oligonucleotides (10 pmol) are radiolabeled by incubating with 5 units T4 polynucleotide kinase and ˜3-6 pmol (˜20-40 mCi) [γ-32P]-ATP in 1× T4 polynucleotide kinase reaction buffer at 37° C. for 30 min, in a 50 μL reaction. After heat inactivation (65° C. for 20 min), reactions are purified through a column to remove unincorporated label. Duplex substrates (100 nM) are generated by annealing labeled oligonucleotides with equimolar amounts of unlabeled complementary oligonucleotide at 95° C. for 3 min, followed by slow cooling to room temperature. For cleavage assays, gRNA molecules are annealed by heating to 95° C. for 30 s, followed by slow cooling to room temperature. Cas9 (500 nM final concentration) is pre-incubated with the annealed gRNA molecules (500 nM) in cleavage assay buffer (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 5% glycerol) in a total volume of 9 μl. Reactions are initiated by the addition of 1 μl target DNA (10 nM) and incubated for 1 h at 37° C. Reactions are quenched by the addition of 20 μl of loading dye (5 mM EDTA, 0.025% SDS, 5% glycerol in formamide) and heated to 95° C. for 5 min. Cleavage products are resolved on 12% denaturing polyacrylamide gels containing 7 M urea and visualized by phosphorimaging. The resulting cleavage products indicate that whether the complementary strand, the non-complementary strand, or both, are cleaved.

One or both of these assays can be used to evaluate the suitability of a candidate gRNA molecule or candidate Cas9 molecule.

Binding Assay: Testing the Binding of Cas9 Molecule to Target DNA

Exemplary methods for evaluating the binding of Cas9 molecule to target DNA are described, e.g., in Jinek 2012.

For example, in an electrophoretic mobility shift assay, target DNA duplexes are formed by mixing of each strand (10 nmol) in deionized water, heating to 95° C. for 3 min and slow cooling to room temperature. All DNAs are purified on 8% native gels containing 1× TBE. DNA bands are visualized by UV shadowing, excised, and eluted by soaking gel pieces in DEPC-treated H₂O. Eluted DNA is ethanol precipitated and dissolved in DEPC-treated H₂O. DNA samples are 5′ end labeled with [γ-32P]-ATP using T4 polynucleotide kinase for 30 min at 37° C. Polynucleotide kinase is heat denatured at 65° C. for 20 min, and unincorporated radiolabel is removed using a column. Binding assays are performed in buffer containing 20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl₂, 1 mM DTT and 10% glycerol in a total volume of 10 μl. Cas9 protein molecule is programmed with equimolar amounts of pre-annealed gRNA molecule and titrated from 100 pM to 1 μM. Radiolabeled DNA is added to a final concentration of 20 pM. Samples are incubated for 1 h at 37° C. and resolved at 4° C. on an 8% native polyacrylamide gel containing 1× TBE and 5 mM MgCl₂. Gels are dried and DNA visualized by phosphorimaging.

Differential Scanning Flourimetry (DSF)

The thermostability of Cas9-gRNA ribonucleoprotein (RNP) complexes can be measured via DSF. This technique measures the thermostability of a protein, which can increase under favorable conditions such as the addition of a binding RNA molecule, e.g., a gRNA.

The assay is performed using two different protocols, one to test the best stoichiometric ratio of gRNA:Cas9 protein and another to determine the best solution conditions for RNP formation.

To determine the best solution to form RNP complexes, a 2 uM solution of Cas9 in water+10× SYPRO Orange® (Life Technologies cat #S-6650) and dispensed into a 384 well plate. An equimolar amount of gRNA diluted in solutions with varied pH and salt is then added. After incubating at room temperature for 10′ and brief centrifugation to remove any bubbles, a Bio-Rad CFX384™ Real-Time System C1000 Touch™ Thermal Cycler with the Bio-Rad CFX Manager software is used to run a gradient from 20° C. to 90° C. with a 1° increase in temperature every 10 seconds.

The second assay consists of mixing various concentrations of gRNA with 2 uM Cas9 in optimal buffer from assay 1 above and incubating at RT for 10′ in a 384 well plate. An equal volume of optimal buffer+10× SYPRO Orange® (Life Technologies cat #S-6650) is added and the plate sealed with Microseal® B adhesive (MSB-1001). Following brief centrifugation to remove any bubbles, a Bio-Rad CFX384™ Real-Time System C1000 Touch™ Thermal Cycler with the Bio-Rad CFX Manager software is used to run a gradient from 20° C. to 90° C. with a 1° increase in temperature every 10 seconds.

VI. Genome Editing Approaches

While not wishing to be bound by theory, altering the LCA10 target position may be achieved using one of the approaches discussed herein.

NHEJ Approaches for Gene Targeting

As described herein, nuclease-induced non-homologous end-joining (NHEJ) can be used to introduce indels at a target position. Nuclease-induced NHEJ can also be used to remove (e.g., delete) genomic sequence including the mutation at a target position in a gene of interest.

While not wishing to be bound by theory, it is believed that, in an embodiment, the genomic alterations associated with the methods described herein rely on nuclease-induced NHEJ and the error-prone nature of the NHEJ repair pathway. NHEJ repairs a double-strand break in the DNA by joining together the two ends; however, generally, the original sequence is restored only if two compatible ends, exactly as they were formed by the double-strand break, are perfectly ligated. The DNA ends of the double-strand break are frequently the subject of enzymatic processing, resulting in the addition or removal of nucleotides, at one or both strands, prior to rejoining of the ends. This results in the presence of insertion and/or deletion (indel) mutations in the DNA sequence at the site of the NHEJ repair.

The indel mutations generated by NHEJ are unpredictable in nature; however, at a given break site certain indel sequences are favored and are over represented in the population, likely due to small regions of microhomology. The lengths of deletions can vary widely; most commonly in the 1-50 bp range, but they can easily reach greater than 100-200 bp. Insertions tend to be shorter and often include short duplications of the sequence immediately surrounding the break site. However, it is possible to obtain large insertions, and in these cases, the inserted sequence has often been traced to other regions of the genome or to plasmid DNA present in the cells.

Because NHEJ is a mutagenic process, it can also be used to delete small sequence motifs as long as the generation of a specific final sequence is not required. If a double-strand break is targeted near to a short target sequence, the deletion mutations caused by the NHEJ repair often span, and therefore remove, the unwanted nucleotides. For the deletion of larger DNA segments, introducing two double-strand breaks, one on each side of the sequence, can result in NHEJ between the ends with removal of the entire intervening sequence. Both of these approaches can be used to delete specific DNA sequences; however, the error-prone nature of NHEJ may still produce indel mutations at the site of deletion.

Both double strand cleaving eaCas9 molecules and single strand, or nickase, eaCas9 molecules can be used in the methods and compositions described herein to generate break-induced indels.

Double Strand Break

In an embodiment, double strand cleavage is effected by a Cas9 molecule having cleavage activity associated with an HNH-like domain and cleavage activity associated with a RuvC-like domain, e.g., an N-terminal RuvC-like domain, e.g., a wild type Cas9. Such embodiments require only a single gRNA.

Single Strand Break

In other embodiments, two single strand breaks are effected by a Cas9 molecule having nickase activity, e.g., cleavage activity associated with an HNH-like domain or cleavage activity associated with an N-terminal RuvC-like domain. Such embodiments require two gRNAs, one for placement of each single strand break. In an embodiment, the Cas9 molecule having nickase activity cleaves the strand to which the gRNA hybridizes, but not the strand that is complementary to the strand to which the gRNA hybridizes. In an embodiment, the Cas9 molecule having nickase activity does not cleave the strand to which the gRNA hybridizes, but rather cleaves the strand that is complementary to the strand to which the gRNA hybridizes.

In an embodiment, the nickase has HNH activity, e.g., a Cas9 molecule having the RuvC activity inactivated, e.g., a Cas9 molecule having a mutation at D10, e.g., the D10A mutation. D10A inactivates RuvC therefore the Cas9 nickase has (only) HNH activity and will cut on the strand to which the gRNA hybridizes (the complementary strand, which does not have the NGG PAM on it). In other embodiments, a Cas9 molecule having an H840, e.g., an H840A, mutation can be used as a nickase. H840A inactivates HNH therefore the Cas9 nickase has (only) RuvC activity and cuts on the non-complementary strand (the strand that has the NGG PAM and whose sequence is identical to the gRNA). In other embodiments, a Cas9 molecule having an H863, e.g., an H863A, mutation can be used as a nickase. H863A inactivates HNH therefore the Cas9 nickase has (only) RuvC activity and cuts on the non-complementary strand (the strand that has the NGG PAM and whose sequence is identical to the gRNA).

In an embodiment, in which a nickase and two gRNAs are used to position two single strand breaks, one nick is on the + strand and one nick is on the − strand of the target nucleic acid. The PAMs can be outwardly facing. The gRNAs can be selected such that the gRNAs are separated by, from 0-50, 0-100, or 0-200 nucleotides. In an embodiment, there is no overlap between the target sequences that are complementary to the targeting domains of the two gRNAs. In an embodiment, the gRNAs do not overlap and are separated by as much as 50, 100, or 200 nucleotides. In an embodiment, the use of two gRNAs can increase specificity, e.g., by decreasing off-target binding (Ran 2013).

Placement of Double Strand or Single Strand Breaks Relative to the Target Position

In an embodiment, in which a gRNA and Cas9 nuclease generate a double strand break for the purpose of inducing break-induced indels, a gRNA, e.g., a unimolecular (or chimeric) or modular gRNA molecule, is configured to position one double-strand break in close proximity to a nucleotide of the target position. In an embodiment, the cleavage site is between 0-40 bp away from the target position (e.g., less than 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 bp from the target position).

In an embodiment, in which two gRNAs complexing with a Cas9 nickase induce two single strand breaks for the purpose of introducing break-induced indels, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position two single-strand breaks to provide for NHEJ-mediated alteration of a nucleotide of the target position. In an embodiment, the gRNAs are configured to position cuts at the same position, or within a few nucleotides of one another, on different strands, essentially mimicking a double strand break. In an embodiment, the two nicks are between 0-40 bp away from the target position (e.g., less than 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 bp from the target position) respectively, and the two single strand breaks are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50 , 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp). In an embodiment, the gRNAs are configured to place a single strand break on either side of the target position. In an embodiment, the gRNAs are configured to place a single strand break on the same side (either 5′ or 3′) of the target position.

Regardless of whether a break is a double strand or a single strand break, the gRNA should be configured to avoid unwanted target chromosome elements, such as repeated elements, e.g., an Alu repeat, in the target domain. In addition, a break, whether a double strand or a single strand break, should be sufficiently distant from any sequence that should not be altered. For example, cleavage sites positioned within introns should be sufficiently distant from any intron/exon border, or naturally occurring splice signal, to avoid alteration of the exonic sequence or unwanted splicing events.

Single-Strand Annealing

Single strand annealing (SSA) is another DNA repair process that repairs a double-strand break between two repeat sequences present in a target nucleic acid. Repeat sequences utilized by the SSA pathway are generally greater than 30 nucleotides in length. Resection at the break ends occurs to reveal repeat sequences on both strands of the target nucleic acid. After resection, single strand overhangs containing the repeat sequences are coated with RPA protein to prevent the repeats sequences from inappropriate annealing, e.g., to themselves. RAD52 binds to and each of the repeat sequences on the overhangs and aligns the sequences to enable the annealing of the complementary repeat sequences. After annealing, the single-strand flaps of the overhangs are cleaved. New DNA synthesis fills in any gaps, and ligation restores the DNA duplex. As a result of the processing, the DNA sequence between the two repeats is deleted. The length of the deletion can depend on many factors including the location of the two repeats utilized, and the pathway or processivity of the resection.

In contrast to HDR pathways, SSA does not require a template nucleic acid to alter or correct a target nucleic acid sequence. Instead, the complementary repeat sequence is utilized.

Other DNA Repair Pathways SSBR (Single Strand Break Repair)

Single-stranded breaks (SSB) in the genome are repaired by the SSBR pathway, which is a distinct mechanism from the DSB repair mechanisms discussed above. The SSBR pathway has four major stages: SSB detection, DNA end processing, DNA gap filling, and DNA ligation. A more detailed explanation is given in Caldecott, Nature Reviews Genetics 9, 619-631 (August 2008), and a summary is given here.

In the first stage, when a SSB forms, PARP1 and/or PARP2 recognize the break and recruit repair machinery. The binding and activity of PARP1 at DNA breaks is transient and it seems to accelerate SSBr by promoting the focal accumulation or stability of SSBr protein complexes at the lesion. Arguably the most important of these SSBr proteins is XRCC1, which functions as a molecular scaffold that interacts with, stabilizes, and stimulates multiple enzymatic components of the SSBr process including the protein responsible for cleaning the DNA 3′ and 5′ ends. For instance, XRCC1 interacts with several proteins (DNA polymerase beta, PNK, and three nucleases, APE1, APTX, and APLF) that promote end processing. APE1 has endonuclease activity. APLF exhibits endonuclease and 3′ to 5′ exonuclease activities. APTX has endonuclease and 3′ to 5′ exonuclease activity.

This end processing is an important stage of SSBR since the 3′- and/or 5′-termini of most, if not all, SSBs are ‘damaged’. End processing generally involves restoring a damaged 3′-end to a hydroxylated state and and/or a damaged 5′ end to a phosphate moiety, so that the ends become ligation-competent. Enzymes that can process damaged 3′ termini include PNKP, APE1, and TDP1. Enzymes that can process damaged 5′ termini include PNKP, DNA polymerase beta, and APTX. LIG3 (DNA ligase III) can also participate in end processing. Once the ends are cleaned, gap filling can occur.

At the DNA gap filling stage, the proteins typically present are PARP1, DNA polymerase beta, XRCC1, FEN1 (flap endonuclease 1), DNA polymerase delta/epsilon, PCNA, and LIG1. There are two ways of gap filling, the short patch repair and the long patch repair. Short patch repair involves the insertion of a single nucleotide that is missing. At some SSBs, “gap filling” might continue displacing two or more nucleotides (displacement of up to 12 bases have been reported). FEN1 is an endonuclease that removes the displaced 5′-residues. Multiple DNA polymerases, including Pol β, are involved in the repair of SSBs, with the choice of DNA polymerase influenced by the source and type of SSB.

In the fourth stage, a DNA ligase such as LIG1 (Ligase I) or LIG3 (Ligase III) catalyzes joining of the ends. Short patch repair uses Ligase III and long patch repair uses Ligase I.

Sometimes, SSBR is replication-coupled. This pathway can involve one or more of CtIP, MRN, ERCC1, and FEN1. Additional factors that may promote SSBR include: aPARP, PARP1, PARP2, PARG, XRCC1, DNA polymerase b, DNA polymerase d, DNA polymerase e, PCNA, LIG1, PNK, PNKP, APE1, APTX, APLF, TDP1, LIG3, FEN1, CtIP, MRN, and ERCC1.

MMR (Mismatch Repair)

Cells contain three excision repair pathways: MMR, BER, and NER. The excision repair pathways have a common feature in that they typically recognize a lesion on one strand of the DNA, then exo/endonucleases remove the lesion and leave a 1-30 nucleotide gap that is sub-sequentially filled in by DNA polymerase and finally sealed with ligase. A more complete picture is given in Li 2008, and a summary is provided here.

Mismatch repair (MMR) operates on mispaired DNA bases.

The MSH2/6 or MSH2/3 complexes both have ATPases activity that plays an important role in mismatch recognition and the initiation of repair. MSH2/6 preferentially recognizes base-base mismatches and identifies mispairs of 1 or 2 nucleotides, while MSH2/3 preferentially recognizes larger ID mispairs.

hMLH1 heterodimerizes with hPMS2 to form hMutLa which possesses an ATPase activity and is important for multiple steps of MMR. It possesses a PCNA/replication factor C (RFC)-dependent endonuclease activity which plays an important role in 3′ nick-directed MMR involving EXO1 (EXO1 is a participant in both HR and MMR). It regulates termination of mismatch-provoked excision. Ligase I is the relevant ligase for this pathway. Additional factors that may promote MMR include: EXO1, MSH2, MSH3, MSH6, MLH1, PMS2, MLH3, DNA Pol d, RPA, HMGB1, RFC, and DNA ligase I.

Base Excision Repair (BER)

The base excision repair (BER) pathway is active throughout the cell cycle; it is responsible primarily for removing small, non-helix-distorting base lesions from the genome. In contrast, the related Nucleotide Excision Repair pathway (discussed in the next section) repairs bulky helix-distorting lesions. A more detailed explanation is given in Caldecott, Nature Reviews Genetics 9, 619-631 (August 2008), and a summary is given here.

Upon DNA base damage, base excision repair (BER) is initiated and the process can be simplified into five major steps: (a) removal of the damaged DNA base; (b) incision of the subsequent a basic site; (c) clean-up of the DNA ends; (d) insertion of the correct nucleotide into the repair gap; and (e) ligation of the remaining nick in the DNA backbone. These last steps are similar to the SSBR.

In the first step, a damage-specific DNA glycosylase excises the damaged base through cleavage of the N-glycosidic bond linking the base to the sugar phosphate backbone. Then AP endonuclease-1 (APE1) or bifunctional DNA glycosylases with an associated lyase activity incised the phosphodiester backbone to create a DNA single strand break (SSB). The third step of BER involves cleaning-up of the DNA ends. The fourth step in BER is conducted by Pol β that adds a new complementary nucleotide into the repair gap and in the final step XRCC1/Ligase III seals the remaining nick in the DNA backbone. This completes the short-patch BER pathway in which the majority (˜80%) of damaged DNA bases are repaired. However, if the 5′-ends in step 3 are resistant to end processing activity, following one nucleotide insertion by Pol β there is then a polymerase switch to the replicative DNA polymerases, Pol δ/ε, which then add ˜2-8 more nucleotides into the DNA repair gap. This creates a 5′-flap structure, which is recognized and excised by flap endonuclease-1 (FEN-1) in association with the processivity factor proliferating cell nuclear antigen (PCNA). DNA ligase I then seals the remaining nick in the DNA backbone and completes long-patch BER. Additional factors that may promote the BER pathway include: DNA glycosylase, APE1, Polb, Pold, Pole, XRCC1, Ligase III, FEN-1, PCNA, RECQL4, WRN, MYH, PNKP, and APTX.

Nucleotide Excision Repair (NER)

Nucleotide excision repair (NER) is an important excision mechanism that removes bulky helix-distorting lesions from DNA. Additional details about NER are given in Marteijn 2014, and a summary is given here. NER a broad pathway encompassing two smaller pathways: global genomic NER (GG-NER) and transcription coupled repair NER (TC-NER). GG-NER and TC-NER use different factors for recognizing DNA damage. However, they utilize the same machinery for lesion incision, repair, and ligation.

Once damage is recognized, the cell removes a short single-stranded DNA segment that contains the lesion. Endonucleases XPF/ERCC1 and XPG (encoded by ERCCS) remove the lesion by cutting the damaged strand on either side of the lesion, resulting in a single-strand gap of 22-30 nucleotides. Next, the cell performs DNA gap filling synthesis and ligation. Involved in this process are: PCNA, RFC, DNA Pol δ, DNA Pol ε or DNA Pol κ, and DNA ligase I or XRCC1/Ligase III. Replicating cells tend to use DNA pol ε and DNA ligase I, while non-replicating cells tend to use DNA Pol δ, DNA Pol κ, and the XRCC1/Ligase III complex to perform the ligation step.

NER can involve the following factors: XPA-G, POLH, XPF, ERCC1, XPA-G, and LIG1. Transcription-coupled NER (TC-NER) can involve the following factors: CSA, CSB, XPB, XPD, XPG, ERCC1, and TTDA. Additional factors that may promote the NER repair pathway include XPA-G, POLH, XPF, ERCC1, XPA-G, LIG1, CSA, CSB, XPA, XPB, XPC, XPD, XPF, XPG, TTDA, UVSSA, USP7, CETN2, RAD23B, UV-DDB, CAK subcomplex, RPA, and PCNA.

Interstrand Crosslink (ICL)

A dedicated pathway called the ICL repair pathway repairs interstrand crosslinks. Interstrand crosslinks, or covalent crosslinks between bases in different DNA strand, can occur during replication or transcription. ICL repair involves the coordination of multiple repair processes, in particular, nucleolytic activity, translesion synthesis (TLS), and HDR. Nucleases are recruited to excise the ICL on either side of the crosslinked bases, while TLS and HDR are coordinated to repair the cut strands. ICL repair can involve the following factors: endonucleases, e.g., XPF and RAD51C, endonucleases such as RAD51, translesion polymerases, e.g., DNA polymerase zeta and Rev1), and the Fanconi anemia (FA) proteins, e.g., FancJ.

Other Pathways

Several other DNA repair pathways exist in mammals.

Translesion synthesis (TLS) is a pathway for repairing a single stranded break left after a defective replication event and involves translesion polymerases, e.g., DNA pol□ and Rev 1.

Error-free postreplication repair (PRR) is another pathway for repairing a single stranded break left after a defective replication event.

Examples of gRNAs in Genome Editing Methods

gRNA molecules as described herein can be used with Cas9 molecules that cleave both or a single strand to alter the sequence of a target nucleic acid, e.g., of a target position or target genetic signature. gRNA molecules useful in these method are described below.

In an embodiment, the gRNA, e.g., a chimeric gRNA, molecule is configured such that it comprises one or more of the following properties;

a) it can position, e.g., when targeting a Cas9 molecule that makes double strand breaks, a double strand break (i) within 50, 100, 150 or 200 nucleotides of a target position, or (ii) sufficiently close that the target position is within the region of end resection;

b) it has a targeting domain of at least 17 nucleotides, e.g., a targeting domain of (i) 17, (ii) 18, or (iii) 20 nucleotides; and

c)

(i) the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides, e.g., at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides from a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail and proximal domain, or a sequence that differs by no more than 1, 2, 3, 4, 5; 6, 7, 8, 9 or 10 nucleotides therefrom;

(ii) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3′ to the last nucleotide of the second complementarity domain, e.g., at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides from the corresponding sequence of a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis gRNA, or a sequence that differs by no more than 1, 2, 3, 4, 5; 6, 7, 8, 9 or 10 nucleotides therefrom;

(iii) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3′ to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain, e.g., at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides from the corresponding sequence of a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis gRNA, or a sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides therefrom;

iv) the tail domain is at least 10, 15, 20, 25, 30, 35 or 40 nucleotides in length, e.g., it comprises at least 10, 15, 20, 25, 30, 35 or 40 nucleotides from a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail domain; or, or a sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides therefrom; or

(v) the tail domain comprises 15, 20, 25, 30, 35, 40 nucleotides or all of the corresponding portions of a naturally occurring tail domain, e.g., a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail domain.

In an embodiment, the gRNA molecule is configured such that it comprises properties: a(i); and b(i).

In an embodiment, the gRNA molecule is configured such that it comprises properties: a(i); and b(ii).

In an embodiment, the gRNA molecule is configured such that it comprises properties: a(i); and b(iii).

In an embodiment, the gRNA molecule is configured such that it comprises properties: a(ii); and b(i).

In an embodiment, the gRNA molecule is configured such that it comprises properties: a(ii); and b(ii).

In an embodiment, the gRNA molecule is configured such that it comprises properties: a(ii); and b(iii).

In an embodiment, the gRNA molecule is configured such that it comprises properties: b(i); and c(i).

In an embodiment, the gRNA molecule is configured such that it comprises properties: b(i); and c(ii).

In an embodiment, the gRNA molecule is configured such that it comprises properties: b(ii); and c(i).

In an embodiment, the gRNA molecule is configured such that it comprises properties: b(ii); and c(ii).

In an embodiment, the gRNA molecule is configured such that it comprises properties: b(iii); and c(i).

In an embodiment, the gRNA molecule is configured such that it comprises properties: b(iii); and c(ii).

In an embodiment, the gRNA is used with a Cas9 nickase molecule having HNH activity, e.g., a Cas9 molecule having the RuvC activity inactivated, e.g., a Cas9 molecule having a mutation at D10, e.g., the D10A mutation.

In an embodiment, the gRNA is used with a Cas9 nickase molecule having RuvC activity, e.g., a Cas9 molecule having the HNH activity inactivated, e.g., a Cas9 molecule having a mutation at H840, e.g., a H840A.

In an embodiment, the gRNA is used with a Cas9 nickase molecule having RuvC activity, e.g., a Cas9 molecule having the HNH activity inactivated, e.g., a Cas9 molecule having a mutation at H863, e.g., a H863A.

In an embodiment, a pair of gRNA molecules, e.g., a pair of chimeric gRNA molecules, comprising a first and a second gRNA molecule, is configured such that they comprises one or more of the following properties:

a) the first and second gRNA molecules position, e.g., when targeting a Cas9 molecule that makes single strand or double strand breaks:

-   -   (i) as positioned by a first and second gRNA molecule described         herein; or     -   (ii) sufficiently close that the target position is altered when         the break is repaired;

b) one or both, independently, has a targeting domain of at least 17 nucleotides, e.g., a targeting domain of (i) 17, (ii) 18, or (iii) 20 nucleotides; and

c) one or both, independently, has a the tail domain is (i) at least 10, 15, 20, 25, 30, 35 or 40 nucleotides in length or (ii) the tail domain comprises, 15, 20, 25, 30, 35, 40, or all of the corresponding portions of a naturally occurring tail domain, e.g., a naturally occurring S. pyogenes, S. aureus, or S. thermophilus tail domain.

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: a(i); and b(i).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: a(i); and b(ii).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: a(i); and b(iii).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: a(ii); and b(i).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: a(ii); and b(ii).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: a(ii); and b(iii).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: b(i); and c(i).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: b(i); and c(ii).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: b(ii); and c(i).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: b(ii); and c(ii).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: b(iii); and c(i).

In an embodiment, one or both of the gRNA molecules is configured such that it comprises properties: b(iii); and c(ii).

In an embodiment the gRNA is used with a Cas9 nickase molecule having HNH activity, e.g., a Cas9 molecule having the RuvC activity inactivated, e.g., a Cas9 molecule having a mutation at D10, e.g., the D10A mutation.

In an embodiment, the gRNA is used with a Cas9 nickase molecule having RuvC activity, e.g., a Cas9 molecule having the HNH activity inactivated, e.g., a Cas9 molecule having a mutation at H840, e.g., a H840A.

In an embodiment the gRNA is used with a Cas9 nickase molecule having RuvC activity, e.g., a Cas9 molecule having the HNH activity inactivated, e.g., a Cas9 molecule having a mutation at H863, e.g., a H863A.

Targets: Cells

Cas9 molecules and gRNA molecules, e.g., a Cas9 molecule/gRNA molecule complex, can be used to manipulate a cell, e.g., to edit a target nucleic acid, in a wide variety of cells.

In some embodiments, a cell is manipulated by altering one or more target genes, e.g., as described herein. In some embodiments, the expression of one or more target genes (e.g., one or more target genes described herein) is modulated, e.g., in vivo.

In an embodiment, the target cell is a retinal cell, e.g., a cell of the retinal pigment epithelium cell or a photoreceptor cell. In another embodiment, the target cell is a horizontal cell, a bipolar cell, an amacrine cell, or a ganglion cell. In an embodiment, the target cell is a cone photoreceptor cell or cone cell, a rod photoreceptor cell or rod cell, or a macular cone photoreceptor cell. In an exemplary embodiment, cone photoreceptors in the macula are targeted, i.e., cone photoreceptors in the macula are the target cells.

In an embodiment, the target cell is removed from the subject, the gene altered ex vivo, and the cell returned to the subject. In an embodiment, a photoreceptor cell is removed from the subject, the gene altered ex vivo, and the photoreceptor cell returned to the subject. In an embodiment, a cone photoreceptor cell is removed from the subject, the gene altered ex vivo, and the cone photoreceptor cell returned to the subject.

In an embodiment, the cells are induced pluripotent stem cells (iPS) cells or cells derived from iPS cells, e.g., iPS cells from the subject, modified to alter the gene and differentiated into retinal progenitor cells or retinal cells, e.g., retinal photoreceptors, and injected into the eye of the subject, e.g., subretinally, e.g., in the submacular region of the retina.

In an embodiment, the cells are targeted in vivo, e.g., by delivery of the components, e.g., a Cas9 molecule and a gRNA molecule, to the target cells. In an embodiment, the target cells are retinal pigment epithelium, photoreceptor cells, or a combination thereof. In an embodiment, AAV is used to deliver the components, e.g., a Cas9 molecule and a gRNA molecule, e.g., by transducing the target cells.

VII. Delivery, Formulations and Routes of Administration

The components, e.g., a Cas9 molecule and gRNA molecule can be delivered, formulated, or administered in a variety of forms, see, e.g., Table 18. In an embodiment, one Cas9 molecule and two or more (e.g., 2, 3, 4, or more) different gRNA molecules are delivered, e.g., by an AAV vector. In an embodiment, the sequence encoding the Cas9 molecule and the sequence(s) encoding the two or more (e.g., 2, 3, 4, or more) different gRNA molecules are present on the same nucleic acid molecule, e.g., an AAV vector. When a Cas9 or gRNA component is delivered encoded in DNA the DNA will typically include a control region, e.g., comprising a promoter, to effect expression. Useful promoters for Cas9 molecule sequences include CMV, EFS, EF-1a, MSCV, PGK, CAG, hGRK1, hCRX, hNRL, and hRCVRN control promoters. In an embodiment, the promoter is a constitutive promoter. In another embodiment, the promoter is a tissue specific promoter. Exemplary promoter sequences are disclosed in Table 20. Useful promoters for gRNAs include H1, 7SK, and U6 promoters. Promoters with similar or dissimilar strengths can be selected to tune the expression of components. Sequences encoding a Cas9 molecule can comprise a nuclear localization signal (NLS), e.g., an SV40 NLS. In an embodiment, the sequence encoding a Cas9 molecule comprises at least two nuclear localization signals. In an embodiment a promoter for a Cas9 molecule or a gRNA molecule can be, independently, inducible, tissue specific, or cell specific. To detect the expression of a Cas9, an affinity tag can be used. Useful affinity tag sequences include, but are not limited to, 3xFlag tag, single Flag tag, HA tag, Myc tag or HIS tag. Exemplary affinity tag sequences are disclosed in Table 26. To regulate Cas9 expression, e.g., in mammalian cells, polyadenylation signals (poly(A) signals) can be used. Exemplary polyadenylation signals are disclosed in Table 27.

Table 18 provides examples of how the components can be formulated, delivered, or administered.

TABLE 18 Elements Cas9 gRNA Molecule(s) molecule(s) Comments DNA DNA In this embodiment a Cas9 molecule, typically an eaCas9 molecule, and a gRNA are transcribed from DNA. In this embodiment they are encoded on separate molecules. DNA In this embodiment a Cas9 molecule, typically an eaCas9 molecule, and a gRNA are transcribed from DNA, here from a single molecule. DNA RNA In this embodiment a Cas9 molecule, typically an eaCas9 molecule, is transcribed from DNA. mRNA RNA In this embodiment a Cas9 molecule, typically an eaCas9 molecule, is transcribed from DNA. Protein DNA In this embodiment a Cas9 molecule, typically an eaCas9 molecule, is provided as a protein. A gRNA is transcribed from DNA. Protein RNA In this embodiment an eaCas9 molecule is provided as a protein.

Table 19 summarizes various delivery methods for the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component, as described herein.

TABLE 19 Delivery into Type of Non-Dividing Duration of Genome Molecule Delivery Vector/Mode Cells Expression Integration Delivered Physical (e.g., electroporation, YES Transient NO Nucleic Acids particle gun, Calcium and Proteins Phosphate transfection) Viral Retrovirus NO Stable YES RNA Lentivirus YES Stable YES/NO with RNA modifications Adenovirus YES Transient NO DNA Adeno-Associated YES Stable NO DNA Virus (AAV) Vaccinia Virus YES Very Transient NO DNA Herpes Simplex YES Stable NO DNA Virus Non-Viral Cationic YES Transient Depends on Nucleic Acids Liposomes what is and Proteins delivered Polymeric YES Transient Depends on Nucleic Acids Nanoparticles what is and Proteins delivered Biological Attenuated YES Transient NO Nucleic Acids Non-Viral Bacteria Delivery Engineered YES Transient NO Nucleic Acids Vehicles Bacteriophages Mammalian YES Transient NO Nucleic Acids Virus-like Particles Biological YES Transient NO Nucleic Acids liposomes: Erythrocyte Ghosts and Exosomes

Table 20 describes exemplary promoter sequences that can be used in AAV vectors, e.g., for Cas9 expression.

TABLE 20 Cas9 Promoter Sequences Promoter Length (bp) DNA Sequence CMV 617 SEQ ID NO: 401 EFS 252 SEQ ID NO: 402 Human GRK1 292 SEQ ID NO: 403 (rhodopsin kinase) Human CRX (cone 113 SEQ ID NO: 404 rod homeobox transcription factor) Human NRL (neural 281 SEQ ID NO: 405 retina leucine zipper transcription factor enhance upstream of the human TK terminal promoter) Human RCVRN 235 SEQ ID NO: 406 (recoverin)

Table 26 describes exemplary affinity tag sequences that can be used in AAV vectors, e.g., for Cas9 expression.

TABLE 26 Affinity tag Amino Acid Sequence 3XFlag tag DYKDHDGDYKDHDIDYKDDDDK (SEQ ID NO: 426) Flag tag (single) DYKDDDDK (SEQ ID NO: 451) HA tag YPYDVPDYA (SEQ ID NO: 452) Myc tag EQKLISEEDL (SEQ ID NO: 453) HIS tag HHHHHH (SEQ ID NO: 454)

Table 27 describes exemplary polyadenylation (polyA) sequences that can be used in AAV vectors, e.g., for Cas9 expression.

TABLE 27 Exemplary PolyA Sequences PolyA DNA sequence Mini polyA SEQ ID NO: 424 bGH polyA SEQ ID NO: 455 SV40 polyA SEQ ID NO: 456

Table 25 describes exemplary Inverted Terminal Repeat (ITR) sequences that can be used in AAV vectors.

TABLE 25 Sequences of ITRs from Exemplary AAV Serotypes AAV Serotype Left ITR Sequence Right ITR Sequence AAV1 SEQ ID NO: 407 SEQ ID NO: 436 AAV2 SEQ ID NO: 408 SEQ ID NO: 437 AAV3B SEQ ID NO: 409 SEQ ID NO: 438 AAV4 SEQ ID NO: 410 SEQ ID NO: 439 AAV5 SEQ ID NO: 411 SEQ ID NO: 440 AAV6 SEQ ID NO: 412 SEQ ID NO: 441 AAV7 SEQ ID NO: 413 SEQ ID NO: 442 AAV8 SEQ ID NO: 414 SEQ ID NO: 443 AAV9 SEQ ID NO: 415 SEQ ID NO: 444

Additional exemplary sequences for the recombinant AAV genome components described herein are provided below.

Exemplary left and right ITR sequences are provided in Table 25 (SEQ ID NOs: 407-415 and 436-444).

Exemplary spacer 1 sequence: (SEQ ID NO: 416) CAGATCTGAATTCGGTACC. Exemplary U6 promoter sequence: (SEQ ID NO: 417) AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATATTTGCAT ATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAATTTGACTGTAAAC ACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGGG TAGTTTGCAGTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACC GTAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGA CGAAACACC

Exemplary gRNA targeting domain sequences are described herein, e.g., in Tables 2A-2D, Tables 3A-3C, Tables 4A-4D, Tables 5A-5D, Tables 6A-6B, Tables 7A-7D, Tables 8A-8D, Tables 9A-9E, Tables 10A-10B, or Table 11.

Exemplary gRNA scaffold domain sequence: (SEQ ID NO: 418) GTTTTAGTACTCTGGAAACAGAATCTACTAAAACAAGGCAAAATGCCGTGT TTATCTCGTCAACTTGTTGGCGAGATTTTTT. Exemplary spacer 2 domain sequence: (SEQ ID NO: 419) GGTACCGCTAGCGCTTAAGTCGCGATGTACGGGCCAGATATACGCGTTGA.

Exemplary Polymerase II promoter sequences are provided in Table 20.

Exemplary N-ter NLS nucleotide sequence: CCGAAGAAAAAGCGCAAGGTCGAAGCGTCC (SEQ ID NO: 420) Exemplary N-ter NLS amino acid sequence: PKKKRKV (SEQ ID NO: 434) Exemplary S. aureus Cas9 nucleotide sequence set forth in SEQ ID NO: 39. Exemplary S. aureus Cas9 amino acid sequence set forth in SEQ ID NO: 26. Exemplary C-ter NLS sequence: CCCAAGAAGAAGAGGAAAGTC (SEQ ID NO: 422). Exemplary C-ter NLS amino acid sequence: PKKKRKV (SEQ ID NO: 434) Exemplary poly(A) signal sequence: TAGCAATAAAGGATCGTTTATTTTCATTGGAAGCGTGTGTTGGTTTTTTGA TCAGGCGCG (SEQ ID NO: 424). Exemplary Spacer 3 sequence: TCCAAGCTTCGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCGTT AACTCTAGATTTAAATGCATGCTGGGGAGAGATCT (SEQ ID NO: 425) Exemplary 3xFLAG nucleotide sequence: GACTACAAAGACCATGACGGTGATTATAAAGATCATGACATCGATTACAAG GATGACGATGACAAG (SEQ ID NO: 423). Exemplary 3xFLAG amino acid sequence: DYKDHDGDYKDHDIDYKDDDDK (SEQ ID NO: 426) Exemplary Spacer 4 sequence: CGACTTAGTTCGATCGAAGG (SEQ ID NO: 427).

Exemplary recombinant AAV genome sequences are provided in FIGS. 19A-24F (SEQ ID NOs: 428-433 and 445-450). Exemplary sequences of the recombinant AAV genome components (e.g., one or more of the components described above) are also shown in FIGS. 19A-24F (SEQ ID NOs: 428-433 and 445-450).

In certain aspects, the present disclosure focuses on AAV vectors encoding CRISPR/Cas9 genome editing systems, and on the use of such vectors to treat CEP290 associated disease. Exemplary AAV vector genomes are schematized in FIGS. 25A through 25D, which illustrate certain fixed and variable elements of these vectors: inverted terminal repeats (ITRs), one or two gRNA sequences and promoter sequences to drive their expression, a Cas9 coding sequence and another promoter to drive its expression. Each of these elements is discussed in detail below.

Turning first to the gRNA pairs utilized in the nucleic acids or AAV vectors of the present disclosure, one of three “left” or “upstream” guides may be used to cut upstream (between exon 26 and the IVS26 mutation), and one of three “right” or “downstream” guides is used to cut downstream (between the IVS26 mutation and exon 27). Targeting domain sequences of these guides (both DNA and RNA sequences) are presented in Table 28, below:

TABLE 28 Upstream (left) and Downstream (right) gRNA Targeting Domain Sequences SEQ SEQ ID ID NO: DNA NO: RNA Upstream (left) guides 389 GTTCTGTCCTCAGTAAAAGG 530 GUUCUGUCCUCAGUAAAAGG TA UA 390 GAATAGTTTGTTCTGGGTAC 468 GAAUAGUUUGUUCUGGGUAC 391 GAGAAAGGGATGGGCACTTA 538 GAGAAAGGGAUGGGCACUUA Downstream (right) guides 388 GTCAAAAGCTACCGGTTACC 558 GUCAAAAGCUACCGGUUACC TG UG 392 GATGCAGAACTAGTGTAGAC 460 GAUGCAGAACUAGUGUAGAC 394 GAGTATCTCCTGTTTGGCA 568 GAGUAUCUCCUGUUUGGCA

The left and right guides can be used in any combination, though certain combinations may be more suitable for certain applications. Table 29 sets forth several upstream+downstream guide pairs used in the embodiments of this disclosure. It should be noted, notwithstanding the use of “left” and “right” as nomenclature for gRNAs, that any guide in a pair, upstream or downstream, may be placed in either one of the gRNA coding sequence positions illustrated in FIG. 25.

TABLE 29 Upstream (Left) + Downstream (Right) Guide Pairs by SEQ ID NO. Downstream 388 392 394 Upstre 389 389 + 388 389 + 392 389 + 394 390 390 + 388 390 + 392 390 + 394 391 391 + 388 391 + 392 391 + 394 Downstream 558 460 568 Upstream 530 530 + 558 530 + 460 530 + 568 468 468 + 558 468 + 460 468 + 568 538 538 + 558 538 + 460 538 + 568

In some embodiments, the gRNAs used in the present disclosure are derived from S. aureus gRNAs and can be unimolecular or modular, as described below. An exemplary unimolecular S. aureus gRNA is shown in FIG. 18B, and exemplary DNA and RNA sequences corresponding to unimolecular S. aureus gRNAs are shown below:

DNA: (SEQ ID NO: 2785) [N] ₁₆₋₂₄GTTTTAGTACTCTGGAAACAGAATCTACTAAAACAAGGCAAAA TGCCGTGTTTATCTCGTCAACTTGTTGGCGAGATTTTTT and RNA: (SEQ ID NO: 2779) [N] ₁₆₋₂₄GUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGCAAAA UGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUUUU. DNA: (SEQ ID NO: 2787) [N] ₁₆₋₂₄GTTATAGTACTCTGGAAACAGAATCTACTATAACAAGGCAAAA TGCCGTGTTTATCTCGTCAACTTGTTGGCGAGATTTTTT and RNA: (SEQ ID NO: 2786) [N] ₁₆₋₂₄GUUAUAGUACUCUGGAAACAGAAUCUACUAUAACAAGGCAAAA UGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUUUU.

It should be noted that, while the figure depicts a targeting domain of 20 nucleotides, the targeting domain can have any suitable length. gRNAs used in the various embodiments of this disclosure preferably include targeting domains of between 16 and 24 (inclusive) bases in length at their 5′ ends, and optionally include a 3′ U6 termination sequence as illustrated.

The gRNA in FIG. 18B is depicted as unimolecular, but in some instances modular guides can be used. In the exemplary unimolecular gRNA sequences above, a 5′ portion corresponding to a crRNA (underlined) is connected by a GAAA linker to a 3′ portion corresponding to a tracrRNA (double underlined). Skilled artisans will appreciate that two-part modular gRNAs can be used that correspond to the underlined and double underlined sections.

Either one of the gRNAs presented above can be used with any of targeting sequences SEQ ID NOs: 389-391, 388, 392, or 394, and two gRNAs in a pair do not necessarily include the same backbone sequence. Additionally, skilled artisans will appreciate that the exemplary gRNA designs set forth herein can be modified in a variety of ways, which are described below or are known in the art; the incorporation of such modifications is within the scope of this disclosure.

Expression of each of the gRNAs in the AAV vector is driven by a pair of U6 promoters, such as a human U6 promoter. An exemplary U6 promoter sequence, as set forth in Maeder, is SEQ ID NO: 417.

Turning next to Cas9, in some embodiments the Cas9 protein is S. aureus Cas9. In further embodiments of this disclosure an S. aureus Cas9 sequence is modified to include two nuclear localization sequences (NLSs) at the C- and N-termini of the Cas9 protein, and a mini-polyadenylation signal (or Poly-A sequence). Exemplary S. aureus Cas9 sequences are provided as SEQ ID NO: 39 (i.e., codon-optimized S. aureus Cas9 nucleotide sequence) and SEQ ID NO: 26 (i.e., S. aureus Cas9 protein sequence). These sequences are exemplary in nature, and are not intended to be limiting. The skilled artisan will appreciate that modifications of these sequences may be possible or desirable in certain applications; such modifications are described below, or are known in the art, and are within the scope of this disclosure.

Skilled artisans will also appreciate that polyadenylation signals are widely used and known in the art, and that any suitable polyadenylation signal can be used in the embodiments of this disclosure. One exemplary polyadenylation signal is set forth in SEQ ID NO: 424.

Cas9 expression is driven, in certain vectors of this disclosure, by one of three promoters: cytomegalovirus (CMV) (i.e., SEQ ID NO: 401), elongation factor-1 (EFS) (i.e., SEQ ID NO: 402), or human g-protein receptor coupled kinase-1 (hGRK1) (i.e., SEQ ID NO: 403), which is specifically expressed in retinal photoreceptor cells. Modifications of the sequences of the promoters may be possible or desirable in certain applications, and such modifications are within the scope of this disclosure.

AAV genomes according to the present disclosure generally incorporate inverted terminal repeats (ITRs) derived from the AAV2 serotype. Exemplary left and right ITRs are SEQ ID NO: 408 (AAV2 Left ITR) and SEQ ID NO: 437 (AAV2 Right ITR), respectively. It should be noted, however, that numerous modified versions of the AAV2 ITRs are used in the field, and the ITR sequences shown below are exemplary and are not intended to be limiting. Modifications of these sequences are known in the art, or will be evident to skilled artisans, and are thus included in the scope of this disclosure.

As FIG. 25 illustrates, the gRNA pairs and the Cas9 promoter are variable and can be selected from the lists presented above. For clarity, this disclosure encompasses nucleic acids and/or AAV vectors comprising any combination of these elements, though certain combinations may be preferred for certain applications. Accordingly, in various embodiments of this disclosure, a nucleic acid or AAV vector encodes a CMV promoter for the Cas9, and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 388 (RNA sequences are SEQ ID NOs: 530 and 558, respectively); a CMV promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 392 (RNA sequences are SEQ ID NOs: 530 and 460, respectively); a CMV promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 394 (RNA sequences are SEQ ID NOs: 530 and 568, respectively); a CMV promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 388 (RNA sequences are SEQ ID NOs: 468 and 558, respectively); a CMV promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 392 (RNA sequences are SEQ ID NOs: 468 and 460, respectively); a CMV promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 394 (RNA sequences are SEQ ID NOs: 468 and 568, respectively); a CMV promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 388 (RNA sequences are SEQ ID NOs: 538 and 558, respectively); a CMV promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 392 (RNA sequences are SEQ ID NOs: 538 and 460, respectively); a CMV promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 394 (RNA sequences are SEQ ID NOs: 538 and 568, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 388 (RNA sequences are SEQ ID NOs: 530 and 558, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 392 (RNA sequences are SEQ ID NOs: 530 and 460, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 394 (RNA sequences are SEQ ID NOs: 530 and 568, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 388 (RNA sequences are SEQ ID NOs: 468 and 558, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 392 (RNA sequences are SEQ ID NOs: 468 and 460, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 394 (RNA sequences are SEQ ID NOs: 468 and 568, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 388 (RNA sequences are SEQ ID NOs: 538 and 558, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 392 (RNA sequences are SEQ ID NOs: 538 and 460, respectively); an EFS promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 394 (RNA sequences are SEQ ID NOs: 538 and 568, respectively); an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 388 (RNA sequences are SEQ ID NOs: 530 and 558, respectively); an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 392 (RNA sequences are SEQ ID NOs: 530 and 460, respectively); an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 389 and 394 (RNA sequences are SEQ ID NOs: 530 and 568, respectively); an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 388 (RNA sequences are SEQ ID NOs: 468 and 558, respectively); an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 392 (RNA sequences are SEQ ID NOs: 468 and 460, respectively); an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 390 and 394 (RNA sequences are SEQ ID NOs: 468 and 568, respectively); an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 388 (RNA sequences are SEQ ID NOs: 538 and 558, respectively); an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 392 (RNA sequences are SEQ ID NOs: 538 and 460, respectively); or an hGRK1 promoter and gRNAs comprising targeting domains according to SEQ ID NOs: 391 and 394 (RNA sequences are SEQ ID NOs: 538 and 568, respectively).

In various embodiments, the nucleic acid or AAV vector encodes the following: left and right AAV2 ITR sequences, a first U6 promoter to drive expression of a first guide RNA having a sequence selected from SEQ ID NOs: 2785 and 2787 and/or comprising a targeting domain sequence according to one of SEQ ID NOs: 389-391, a second U6 promoter to drive expression of a second guide RNA comprising a sequence selected from SEQ ID NOs: 2785 and 2787 and/or comprising a targeting domain sequence according to one of SEQ ID NOs: 388, 392, and 394, and a CMV promoter to drive expression of an S. aureus Cas9 encoded by SEQ ID NO: 39; or left and right AAV2 ITR sequences, a first U6 promoter to drive expression of a first guide RNA having a sequence selected from SEQ ID NOs: 2785 or 2787 and/or comprising a targeting domain sequence according to one of SEQ ID NOs: 389-391, a second U6 promoter to drive expression of a second guide RNA comprising a sequence selected from SEQ ID NOs: 2785 and 2787 and/or comprising a targeting domain sequence according to one of SEQ ID NOs: 388, 392, and 394, and an hGRK promoter to drive expression of an S. aureus Cas9 encoded by SEQ ID NO: 39; or left and right AAV2 ITR sequences, a first U6 promoter to drive expression of a first guide RNA having a sequence selected from SEQ ID NOs: 2785 and 2787 and/or comprising a targeting domain sequence according to one of SEQ ID NOs: 389-391, a second U6 promoter to drive expression of a second guide RNA comprising a sequence selected from SEQ ID NOs: 2785 or 2787 and/or comprising a targeting domain sequence according to one of SEQ ID NOs: 388, 392, and 394, and an EFS promoter to drive expression of an S. aureus Cas9 encoded by SEQ ID NO: 39.

As shown in FIG. 25D, the nucleic acid or AAV vector may also comprise a Simian virus 40 (SV40) splice donor/splice acceptor (SD/SA) sequence element. In certain embodiments, the SV40 SD/SA element may be positioned between the GRK1 promoter and the Cas9 gene. In certain embodiments, a Kozak consensus sequence may precede the start codon of Cas9 to ensure robust Cas9 expression.

In some embodiments, the nucleic acid or AAV vector shares at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or greater sequence identity with one of the nucleic acids or AAV vectors recited above.

It should be noted that these sequences described above are exemplary, and can be modified in ways that do not disrupt the operating principles of elements they encode. Such modifications, some of which are discussed below, are within the scope of this disclosure. Without limiting the foregoing, skilled artisans will appreciate that the DNA, RNA or protein sequences of the elements of this disclosure may be varied in ways that do not interrupt their function, and that a variety of similar sequences that are substantially similar (e.g., greater than 90%, 95%, 96%, 97%, 98% or 99% sequence similarity, or in the case of short sequences such as gRNA targeting domains, sequences that differ by no more than 1, 2 or 3 nucleotides) can be utilized in the various systems, methods and AAV vectors described herein. Such modified sequences are within the scope of this disclosure.

The AAV genomes described above can be packaged into AAV capsids (for example, AAV5 capsids), which capsids can be included in compositions (such as pharmaceutical compositions) and/or administered to subjects. An exemplary pharmaceutical composition comprising an AAV capsid according to this disclosure can include a pharmaceutically acceptable carrier such as balanced saline solution (BSS) and one or more surfactants (e.g., Tween20) and/or a thermosensitive or reverse-thermo sensitive polymer (e.g., pluronic). Other pharmaceutical formulation elements known in the art may also be suitable for use in the compositions described here.

Compositions comprising AAV vectors according to this disclosure can be administered to subjects by any suitable means, including without limitation injection, for example, subretinal injection. The concentration of AAV vector within the composition is selected to ensure, among other things, that a sufficient AAV dose is administered to the retina of the subject, taking account of dead volume within the injection apparatus and the relatively limited volume that can be safely administered to the retina. Suitable doses may include, for example, 1×10¹¹ viral genomes (vg)/mL, 2×10¹¹ viral genomes (vg)/mL, 3×10¹¹ viral genomes (vg)/mL, 4×10¹¹ viral genomes (vg)/mL, 5×10¹¹ viral genomes (vg)/mL, 6×10¹¹ viral genomes (vg)/mL, 7×10¹¹ viral genomes (vg)/mL, 8×10¹¹ viral genomes (vg)/mL, 9×10¹¹ viral genomes (vg)/mL, 1×10¹² vg/mL, 2×10¹² viral genomes (vg)/mL, 3×10¹² viral genomes (vg)/mL, 4×10¹² viral genomes (vg)/mL, 5×10¹² viral genomes (vg)/mL, 6×10¹² viral genomes (vg)/mL, 7×10¹² viral genomes (vg)/mL, 8×10¹² viral genomes (vg)/mL, 9×10¹² viral genomes (vg)/mL, 1×10¹³ vg/mL, 2×10¹³ viral genomes (vg)/mL, 3×10¹³ viral genomes (vg)/mL, 4×10¹³ viral genomes (vg)/mL, 5×10¹³ viral genomes (vg)/mL, 6×10¹³ viral genomes (vg)/mL, 7×10¹³ viral genomes (vg)/mL, 8×10¹³ viral genomes (vg)/mL, or 9×10¹³ viral genomes (vg)/mL. Any suitable volume of the composition may be delivered to the subretinal space. In some instances, the volume is selected to form a bleb in the subretinal space, for example 1 microliter, 10 microliters, 50 microliters, 100 microliters, 150 microliters, 200 microliters, 250 microliters, 300 microliters, etc. Any region of the retina may be targeted, though the fovea (which extends approximately 1 degree out from the center of the eye) may be preferred in certain instances due to its role in central visual acuity and the relatively high concentration of cone photoreceptors there relative to peripheral regions of the retina. Alternatively or additionally, injections may be targeted to parafoveal regions (extending between approximately 2 and 10 degrees off center), which are characterized by the presence of all three types of retinal photoreceptor cells. In addition, injections into the parafoveal region may be made at comparatively acute angles using needle paths that cross the midline of the retina. For instance, injection paths may extend from the nasal aspect of the sclera near the limbus through the vitreal chamber and into the parafoveal retina on the temporal side, from the temporal aspect of the sclera to the parafoveal retina on the nasal side, from a portion of the sclera located superior to the cornea to an inferior parafoveal position, and/or from an inferior portion of the sclera to a superior parafoveal position. The use of relatively small angles of injection relative to the retinal surface may advantageously reduce or limit the potential for spillover of vector from the bleb into the vitreous body and, consequently, reduce the loss of the vector during delivery. In other cases, the macula (inclusive of the fovea) can be targeted, and in other cases, additional retinal regions can be targeted, or can receive spillover doses.

To mitigate ocular inflammation and associated discomfort, one or more corticosteroids may be administered before, during, and/or after administration of the composition comprising AAV vectors. In certain embodiments, the corticosteroid may be an oral corticosteroid. In certain embodiments, the oral corticosteroid may be prednisone. In certain embodiments, the corticosteroid may be administered as a prophylactic, prior to administration of the composition comprising AAV vectors. For example, the corticosteroid may be administered the day prior to administration, or 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, or 14 days prior to administration of the composition comprising AAV vectors. In certain embodiments, the corticosteroid may be administered for 1 week to 10 weeks after administration of the composition comprising AAV vectors (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, or 10 weeks after administration of the composition comprising AAV vectors). In certain embodiments, the corticosteroid treatment may be administered prior to (e.g., the day prior to administration, or 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, or 14 days prior to administration) and after administration of the composition comprising AAV vectors (e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 9 weeks, or 10 weeks after administration). For example, the corticosteroid treatment may be administered beginning 3 days prior to until 6 weeks after administration of the AAV vector.

Suitable doses of corticosteroids may include, for example, 0.1 mg/kg/day to 10 mg/kd/day (e.g., 0.1 mg/kg/day, 0.2 mg/kg/day, 0.3 mg/kg/day, 0.4 mg/kg/day, 0.5 mg/kg/day, 0.6 mg/kg/day, 0.7 mg/kg/day, 0.8 mg/kg/day, 0.9 mg/kg/day, or 1.0 mg/kg/day). In certain embodiments, the corticosteroid may be administered at an elevated dose during the corticosteroid treatment, followed by a tapered dose of the corticosteroid. For example, 0.5 mg/kg/day corticosteroid may be administered for 4 weeks, followed by a 15-day taper (0.4 mg/kg/day for 5 days, and then 0.2 mg/kg/day for 5 days, and then 0.1 mg/kg/day for 5 days). The corticosteroid dose may be increased if there is an increase in vitreous inflammation by 1+ on the grading scale following surgery (e.g., within 4 weeks after surgery). For example, if there is an increase in vitreous inflammation by 1+ on the grading scale while the patient is receiving a 0.5 mg/kg/day dose (e.g., within 4 weeks after surgery), the corticosteroid dose may be may be increased to 1 mg/kg/day. If any inflammation is present within 4 weeks after surgery, the taper may be delayed.

For pre-clinical development purposes, systems, compositions, nucleotides and vectors according to this disclosure can be evaluated ex vivo using a retinal explant system, or in vivo using an animal model such as a mouse, rabbit, pig, nonhuman primate, etc. Retinal explants are optionally maintained on a support matrix, and AAV vectors can be delivered by injection into the space between the photoreceptor layer and the support matrix, to mimic subretinal injection. Tissue for retinal explantation can be obtained from human or animal subjects, for example mouse.

Explants are particularly useful for studying the expression of gRNAs and/or Cas9 following viral transduction, and for studying genome editing over comparatively short intervals. These models also permit higher throughput than may be possible in animal models, and can be predictive of expression and genome editing in animal models and subjects. Small (mouse, rat) and large animal models (such as rabbit, pig, nonhuman primate) can be used for pharmacological and/or toxicological studies and for testing the systems, nucleotides, vectors and compositions of this disclosure under conditions and at volumes that approximate those that will be used in clinic. Because model systems are selected to recapitulate relevant aspects of human anatomy and/or physiology, the data obtained in these systems will generally (though not necessarily) be predictive of the behavior of AAV vectors and compositions according to this disclosure in human and animal subjects.

While the foregoing exemplary embodiments have focused on guide RNAs, nucleic acids and AAV vectors targeted to the CEP290 gene, it will be appreciated by those of skill in the art that the nucleic acids and vectors of this disclosure may be used in the editing of other gene targets and the treatment of other diseases such as hereditary retinopathies that may be treated by editing of genes other than CEP290. In certain embodiments, it is contemplated that the same configuration of the nucleic acids or AAV vectors disclosed herein may be used to treat other inherited retinal diseases by modifying the gRNA targeting domains to target and alter the gene of interest.

FIGS. 25A-25D illustrate exemplary AAV vectors that may be used to transduce retinal cells, including without limitation retinal photoreceptor cells such as rod photoreceptors and/or cone photoreceptors, and/or other retinal cell types. The AAV genome of FIG. 25A comprises two guide RNAs comprising targeting domains according to one of the guide pairs of SEQ ID NOs: 389 and 388, SEQ ID NOs: 389 and 392, SEQ ID NOs: 389 and 394, SEQ ID NOs: 390 and 388, SEQ ID NOs: 390 and 392, SEQ ID NOs: 390 and 394, SEQ ID NOs: 391 and 388, SEQ ID NOs: 391 and 392, SEQ ID NOs: 391 and 394, and a promoter sequence according to one of CMV, EFS, hGRK1 driving expression of an S. aureus Cas9 comprising one or two nuclear localization signals and a polyadenylation signal. The vector may additionally include ITRs such as AAV2 ITRs, or other sequences that may be selected for the specific application to which the vector will be employed. A more detailed version of FIG. 25A is shown in FIG. 25D, illustrating that the AAV genome may also comprise a Simian virus 40 (SV40) splice donor/splice acceptor (SD/SA) sequence element. In certain embodiments, the SV40 SD/SA element may be positioned between the promoter and the Cas9 gene. In certain embodiments, a Kozak consensus sequence may precede the start codon of Cas9. The AAV genome of FIG. 25B comprises two guide RNAs according to SEQ ID NOs: 2785 or 2787, and a promoter sequence according to one of SEQ ID NOs: 401-403 driving expression of an S. aureus Cas9 comprising one or two nuclear localization signals and, optionally, a polyadenylation signal. The vector may additionally include ITRs such as AAV2 ITRs, or other sequences that may be selected for the specific application to which the vector will be employed. As is shown in FIG. 25C, other vectors within the scope of this disclosure may include only 1 guide RNA. Thus, in specific embodiments, an AAV genome of this disclosure may encode a CMV promoter for the Cas9 and one guide RNA having a sequence comprising, or sharing at least 90% sequence identity with, a sequence selected from SEQ ID NOs: 2785 and 2787; a CMV promoter for the Cas9 and two guide RNAs, each having a sequence comprising, or sharing at least 90% sequence identity with, a sequence selected from SEQ ID NOs: 2785 and 2787; an hGRK promoter for the Cas9 and one guide RNA having a sequence comprising, or sharing at least 90% sequence identity with, a sequence selected from SEQ ID NOs: 2785 and 2787; an hGRK promoter for the Cas9 and two guide RNAs, each having a sequence comprising, or sharing at least 90% sequence identity with, a sequence selected from SEQ ID NOs: 2785 and 2787; an EFS promoter for the Cas9 and one guide RNA having a sequence comprising, or sharing at least 90% sequence identity with, a sequence selected from SEQ ID NOs: 2785 and 2787; an EFS promoter for the Cas9 and two guide RNAs, each having a sequence comprising, or sharing at least 90% sequence identity with, a sequence selected from SEQ ID NOs: 2785 and 2787.

DNA-Based Delivery of a Cas9 Molecule and/or a gRNA Molecule

Nucleic acids encoding Cas9 molecules (e.g., eaCas9 molecules) and/or gRNA molecules, can be administered to subjects or delivered into cells by art-known methods or as described herein. For example, Cas9-encoding and/or gRNA-encoding DNA can be delivered, e.g., by vectors (e.g., viral or non-viral vectors), non-vector based methods (e.g., using naked DNA or DNA complexes), or a combination thereof.

DNA encoding Cas9 molecules (e.g., eaCas9 molecules) and/or gRNA molecules can be conjugated to molecules (e.g., N-acetylgalactosamine) promoting uptake by the target cells (e.g., the target cells described herein). Donor template molecules can be conjugated to molecules (e.g., N-acetylgalactosamine) promoting uptake by the target cells (e.g., the target cells described herein).

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a vector (e.g., viral vector/virus or plasmid).

A vector can comprise a sequence that encodes a Cas9 molecule and/or a gRNA molecule. A vector can also comprise a sequence encoding a signal peptide (e.g., for nuclear localization, nucleolar localization, mitochondrial localization), fused, e.g., to a Cas9 molecule sequence. For example, a vector can comprise a nuclear localization sequence (e.g., from SV40) fused to the sequence encoding the Cas9 molecule.

One or more regulatory/control elements, e.g., a promoter, an enhancer, an intron, a polyadenylation signal, a Kozak consensus sequence, internal ribosome entry sites (IRES), a 2A sequence, and splice acceptor or donor can be included in the vectors. In some embodiments, the promoter is recognized by RNA polymerase II (e.g., a CMV promoter). In other embodiments, the promoter is recognized by RNA polymerase III (e.g., a U6 promoter). In some embodiments, the promoter is a regulated promoter (e.g., inducible promoter). In other embodiments, the promoter is a constitutive promoter. In some embodiments, the promoter is a tissue specific promoter. In some embodiments, the promoter is a viral promoter. In other embodiments, the promoter is a non-viral promoter.

In some embodiments, the vector or delivery vehicle is a viral vector (e.g., for generation of recombinant viruses). In some embodiments, the virus is a DNA virus (e.g., dsDNA or ssDNA virus). In other embodiments, the virus is an RNA virus (e.g., an ssRNA virus). Exemplary viral vectors/viruses include, e.g., retroviruses, lentiviruses, adenovirus, adeno-associated virus (AAV), vaccinia viruses, poxviruses, and herpes simplex viruses.

In some embodiments, the virus infects dividing cells. In other embodiments, the virus infects non-dividing cells. In some embodiments, the virus infects both dividing and non-dividing cells. In some embodiments, the virus can integrate into the host genome. In some embodiments, the virus is engineered to have reduced immunity, e.g., in human. In some embodiments, the virus is replication-competent. In other embodiments, the virus is replication-defective, e.g., having one or more coding regions for the genes necessary for additional rounds of virion replication and/or packaging replaced with other genes or deleted. In some embodiments, the virus causes transient expression of the Cas9 molecule and/or the gRNA molecule. In other embodiments, the virus causes long-lasting, e.g., at least 1 week, 2 weeks, 1 month, 2 months, 3 months, 6 months, 9 months, 1 year, 2 years, or permanent expression, of the Cas9 molecule and/or the gRNA molecule. The packaging capacity of the viruses may vary, e.g., from at least about 4 kb to at least about 30 kb, e.g., at least about 5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 30 kb, 35 kb, 40 kb, 45 kb, or 50 kb.

In an embodiment, the viral vector recognizes a specific cell type or tissue. For example, the viral vector can be pseudotyped with a different/alternative viral envelope glycoprotein; engineered with a cell type-specific receptor (e.g., genetic modification(s) of one or more viral envelope glycoproteins to incorporate a targeting ligand such as a peptide ligand, a single chain antibody, or a growth factor); and/or engineered to have a molecular bridge with dual specificities with one end recognizing a viral glycoprotein and the other end recognizing a moiety of the target cell surface (e.g., a ligand-receptor, monoclonal antibody, avidin-biotin and chemical conjugation).

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant retrovirus. In some embodiments, the retrovirus (e.g., Moloney murine leukemia virus) comprises a reverse transcriptase, e.g., that allows integration into the host genome. In some embodiments, the retrovirus is replication-competent. In other embodiments, the retrovirus is replication-defective, e.g., having one of more coding regions for the genes necessary for additional rounds of virion replication and packaging replaced with other genes, or deleted. In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant lentivirus. For example, the lentivirus is replication-defective, e.g., does not comprise one or more genes required for viral replication.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant adenovirus. In some embodiments, the adenovirus is engineered to have reduced immunity in human.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant AAV. In some embodiments, the AAV does not incorporate its genome into that of a host cell, e.g., a target cell as describe herein. In some embodiments, the AAV can incorporate at least part of its genome into that of a host cell, e.g., a target cell as described herein. In some embodiments, the AAV is a self-complementary adeno-associated virus (scAAV), e.g., a scAAV that packages both strands which anneal together to form double stranded DNA. AAV serotypes that may be used in the disclosed methods, include AAV1, AAV2, modified AAV2 (e.g., modifications at Y444F, Y500F, Y730F and/or S662V), AAV3, modified AAV3 (e.g., modifications at Y705F, Y731F and/or T492V), AAV4, AAVS, AAV6, modified AAV6 (e.g., modifications at S663V and/or T492V), AAV8, AAV 8.2, AAV9, AAV rh10, and pseudotyped AAV, such as AAV2/8, AAV2/5 and AAV2/6 can also be used in the disclosed methods. In an embodiment, an AAV capsid that can be used in the methods described herein is a capsid sequence from serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV.rh8, AAV.rh10, AAV.rh32/33, AAV.rh43, AAV.rh64R1, or AAV7m8. Exemplary AAV serotypes and ITR sequences are disclosed in Table 25.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered in a re-engineered AAV capsid, e.g., with 50% or greater, e.g., 60% or greater, 70% or greater, 80% or greater, 90% or greater, or 95% or greater, sequence homology with a capsid sequence from serotypes AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV.rh8, AAV.rh10, AAV.rh32/33, AAV.rh43, or AAV.rh64R1.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a chimeric AAV capsid. Exemplary chimeric AAV capsids include, but are not limited to, AAV9i1, AAV2i8, AAV-DJ, AAV2G9, AAV2i8G9, or AAV8G9.

In an embodiment, the AAV is a self-complementary adeno-associated virus (scAAV), e.g., a scAAV that packages both strands which anneal together to form double stranded DNA.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a hybrid virus, e.g., a hybrid of one or more of the viruses described herein. In an embodiment, the hybrid virus is hybrid of an AAV (e.g., of any AAV serotype), with a Bocavirus, B19 virus, porcine AAV, goose AAV, feline AAV, canine AAV, or MVM.

A packaging cell is used to form a virus particle that is capable of infecting a target cell. Such a cell includes a 293 cell, which can package adenovirus, and a ψ2 cell or a PA317 cell, which can package retrovirus. A viral vector used in gene therapy is usually generated by a producer cell line that packages a nucleic acid vector into a viral particle. The vector typically contains the minimal viral sequences required for packaging and subsequent integration into a host or target cell (if applicable), with other viral sequences being replaced by an expression cassette encoding the protein to be expressed, e.g., Cas9. For example, an AAV vector used in gene therapy typically only possesses inverted terminal repeat (ITR) sequences from the AAV genome which are required for packaging and gene expression in the host or target cell. The missing viral functions can be supplied in trans by the packaging cell line and/or plasmid containing E2A, E4, and VA genes from adenovirus, and plasmid encoding Rep and Cap genes from AAV, as described in “Triple Transfection Protocol.” Henceforth, the viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. In embodiment, the viral DNA is packaged in a producer cell line, which contains E1A and/or E1B genes from adenovirus. The cell line is also infected with adenovirus as a helper. The helper virus (e.g., adenovirus or HSV) or helper plasmid promotes replication of the AAV vector and expression of AAV genes from the plasmid with ITRs. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV.

In an embodiment, the viral vector has the ability of cell type and/or tissue type recognition. For example, the viral vector can be pseudotyped with a different/alternative viral envelope glycoprotein; engineered with a cell type-specific receptor (e.g., genetic modification of the viral envelope glycoproteins to incorporate targeting ligands such as a peptide ligand, a single chain antibody, a growth factor); and/or engineered to have a molecular bridge with dual specificities with one end recognizing a viral glycoprotein and the other end recognizing a moiety of the target cell surface (e.g., ligand-receptor, monoclonal antibody, avidin-biotin and chemical conjugation).

In an embodiment, the viral vector achieves cell type specific expression. For example, a tissue-specific promoter can be constructed to restrict expression of the transgene (Cas 9 and gRNA) in only the target cell. The specificity of the vector can also be mediated by microRNA-dependent control of transgene expression. In an embodiment, the viral vector has increased efficiency of fusion of the viral vector and a target cell membrane. For example, a fusion protein such as fusion-competent hemagglutin (HA) can be incorporated to increase viral uptake into cells. In an embodiment, the viral vector has the ability of nuclear localization. For example, a virus that requires the breakdown of the cell wall (during cell division) and therefore will not infect a non-diving cell can be altered to incorporate a nuclear localization peptide in the matrix protein of the virus thereby enabling the transduction of non-proliferating cells. In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a non-vector based method (e.g., using naked DNA or DNA complexes). For example, the DNA can be delivered, e.g., by organically modified silica or silicate (Ormosil), electroporation, gene gun, sonoporation, magnetofection, lipid-mediated transfection, dendrimers, inorganic nanoparticles, calcium phosphates, or a combination thereof.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a combination of a vector and a non-vector based method. For example, a virosome comprises a liposome combined with an inactivated virus (e.g., HIV or influenza virus), which can result in more efficient gene transfer, e.g., in a respiratory epithelial cell than either a viral or a liposomal method alone.

In an embodiment, the delivery vehicle is a non-viral vector. In an embodiment, the non-viral vector is an inorganic nanoparticle. Exemplary inorganic nanoparticles include, e.g., magnetic nanoparticles (e.g., Fe₃MnO₂) and silica. The outer surface of the nanoparticle can be conjugated with a positively charged polymer (e.g., polyethylenimine, polylysine, polyserine) which allows for attachment (e.g., conjugation or entrapment) of payload. In an embodiment, the non-viral vector is an organic nanoparticle (e.g., entrapment of the payload inside the nanoparticle). Exemplary organic nanoparticles include, e.g., SNALP liposomes that contain cationic lipids together with neutral helper lipids which are coated with polyethylene glycol (PEG) and protamine and nucleic acid complex coated with lipid coating.

Exemplary lipids for gene transfer are shown below in Table 21.

TABLE 21 Lipids Used for Gene Transfer Lipid Abbreviation Feature 1,2-Dioleoyl-sn-glycero-3-phosphatidylcholine DOPC Helper 1,2-Dioleoyl-sn-glycero-3-phosphatidylethanolamine DOPE Helper Cholesterol Helper N-[1-(2,3-Dioleyloxy)prophyl]N,N,N-trimethylammonium DOTMA Cationic chloride 1,2-Dioleoyloxy-3-trimethylammonium-propane DOTAP Cationic Dioctadecylamidoglycylspermine DOGS Cationic N-(3-Aminopropyl)-N,N-dimethyl-2,3-bis(dodecyloxy)-1- GAP-DLRIE Cationic propanaminium bromide Cetyltrimethylammonium bromide CTAB Cationic 6-Lauroxyhexyl ornithinate LHON Cationic 1-(2,3-Dioleoyloxypropyl)-2,4,6-trimethylpyridinium 2Oc Cationic 2,3-Dioleyloxy-N-[2(sperminecarboxamido-ethyl]-N,N-dimethyl- DOSPA Cationic 1-propanaminium trifluoroacetate 1,2-Dioleyl-3-trimethylammonium-propane DOPA Cationic N-(2-Hydroxyethyl)-N,N-dimethyl-2,3-bis(tetradecyloxy)-1- MDRIE Cationic propanaminium bromide Dimyristooxypropyl dimethyl hydroxyethyl ammonium bromide DMRI Cationic 3β-[N-(N′,N′-Dimethylaminoethane)-carbamoyl]cholesterol DC-Chol Cationic Bis-guanidium-tren-cholesterol BGTC Cationic 1,3-Diodeoxy-2-(6-carboxy-spermyl)-propylamide DOSPER Cationic Dimethyloctadecylammonium bromide DDAB Cationic Dioctadecylamidoglicylspermidin DSL Cationic rac-[(2,3-Dioctadecyloxypropyl)(2-hydroxyethyl)]- CLIP-1 Cationic dimethylammonium chloride rac-[2(2,3-Dihexadecyloxypropyl- CLIP-6 Cationic oxymethyloxy)ethyl]trimethylammonium bromide Ethyldimyristoylphosphatidylcholine EDMPC Cationic 1,2-Distearyloxy-N,N-dimethyl-3-aminopropane DSDMA Cationic 1,2-Dimyristoyl-trimethylammonium propane DMTAP Cationic O,O′-Dimyristyl-N-lysyl aspartate DMKE Cationic 1,2-Distearoyl-sn-glycero-3-ethylphosphocholine DSEPC Cationic N-Palmitoyl D-erythro-sphingosyl carbamoyl-spermine CCS Cationic N-t-Butyl-N0-tetradecyl-3-tetradecylaminopropionamidine diC14-amidine Cationic Octadecenolyoxy[ethyl-2-heptadecenyl-3 hydroxyethyl] DOTIM Cationic imidazolinium chloride N1-Cholesteryloxycarbonyl-3,7-diazanonane-1,9-diamine CDAN Cationic 2-(3-[Bis(3-amino-propyl)-amino]propylamino)-N- RPR209120 Cationic ditetradecylcarbamoylme-ethyl-acetamide 1,2-dilinoleyloxy-3-dimethylaminopropane DLinDMA Cationic 2,2-dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane DLin-KC2- Cationic DMA dilinoleyl-methyl-4-dimethylaminobutyrate DLin-MC3- Cationic DMA Exemplary polymers for gene transfer are shown below in Table 22.

TABLE 22 Polymers Used for Gene Transfer Polymer Abbreviation Poly(ethylene)glycol PEG Polyethylenimine PEI Dithiobis(succinimidylpropionate) DSP Dimethyl-3,3′-dithiobispropionimidate DTBP Poly(ethylene imine)biscarbamate PEIC Poly(L-lysine) PLL Histidine modified PLL Poly(N-vinylpyrrolidone) PVP Poly(propylenimine) PPI Poly(amidoamine) PAMAM Poly(amidoethylenimine) SS-PAEI Triethylenetetramine TETA Poly(β-aminoester) Poly(4-hydroxy-L-proline ester) PHP Poly(allylamine) Poly(α-[4-aminobutyl]-L-glycolic acid) PAGA Poly(D,L-lactic-co-glycolic acid) PLGA Poly(N-ethyl-4-vinylpyridinium bromide) Poly(phosphazene)s PPZ Poly(phosphoester)s PPE Poly(phosphoramidate)s PPA Poly(N-2-hydroxypropylmethacrylamide) pHPMA Poly (2-(dimethylamino)ethyl methacrylate) pDMAEMA Poly(2-aminoethyl propylene phosphate) PPE-EA Chitosan Galactosylated chitosan N-Dodacylated chitosan Histone Collagen Dextran-spermine D-SPM

In an embodiment, the vehicle has targeting modifications to increase target cell update of nanoparticles and liposomes, e.g., cell specific antigens, monoclonal antibodies, single chain antibodies, aptamers, polymers, sugars, and cell penetrating peptides. In an embodiment, the vehicle uses fusogenic and endosome-destabilizing peptides/polymers. In an embodiment, the vehicle undergoes acid-triggered conformational changes (e.g., to accelerate endosomal escape of the cargo). In an embodiment, a stimuli-cleavable polymer is used, e.g., for release in a cellular compartment. For example, disulfide-based cationic polymers that are cleaved in the reducing cellular environment can be used.

In an embodiment, the delivery vehicle is a biological non-viral delivery vehicle. In an embodiment, the vehicle is an attenuated bacterium (e.g., naturally or artificially engineered to be invasive but attenuated to prevent pathogenesis and expressing the transgene (e.g., Listeria monocytogenes, certain Salmonella strains, Bifidobacterium longum, and modified Escherichia coli), bacteria having nutritional and tissue-specific tropism to target specific tissues, bacteria having modified surface proteins to alter target tissue specificity). In an embodiment, the vehicle is a genetically modified bacteriophage (e.g., engineered phages having large packaging capacity, less immunogenic, containing mammalian plasmid maintenance sequences and having incorporated targeting ligands). In an embodiment, the vehicle is a mammalian virus-like particle. For example, modified viral particles can be generated (e.g., by purification of the “empty” particles followed by ex vivo assembly of the virus with the desired cargo). The vehicle can also be engineered to incorporate targeting ligands to alter target tissue specificity. In an embodiment, the vehicle is a biological liposome. For example, the biological liposome is a phospholipid-based particle derived from human cells (e.g., erythrocyte ghosts, which are red blood cells broken down into spherical structures derived from the subject (e.g., tissue targeting can be achieved by attachment of various tissue or cell-specific ligands), or secretory exosomes—subject (i.e., patient) derived membrane-bound nanovesicle (30-100 nm) of endocytic origin (e.g., can be produced from various cell types and can therefore be taken up by cells without the need of for targeting ligands).

In an embodiment, one or more nucleic acid molecules (e.g., DNA molecules) other than the components of a Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component described herein, are delivered. In an embodiment, the nucleic acid molecule is delivered at the same time as one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered before or after (e.g., less than about 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, 9 hours, 12 hours, 1 day, 2 days, 3 days, 1 week, 2 weeks, or 4 weeks) one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered by a different means than one or more of the components of the Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component, are delivered. The nucleic acid molecule can be delivered by any of the delivery methods described herein. For example, the nucleic acid molecule can be delivered by a viral vector, e.g., an integration-deficient lentivirus, and the Cas9 molecule component and/or the gRNA molecule component can be delivered by electroporation, e.g., such that the toxicity caused by nucleic acids (e.g., DNAs) can be reduced. In an embodiment, the nucleic acid molecule encodes a therapeutic protein, e.g., a protein described herein. In an embodiment, the nucleic acid molecule encodes an RNA molecule, e.g., an RNA molecule described herein.

Delivery of RNA Encoding a Cas9 Molecule

RNA encoding Cas9 molecules (e.g., eaCas9 molecules) and/or gRNA molecules, can be delivered into cells, e.g., target cells described herein, by art-known methods or as described herein. For example, Cas9-encoding and/or gRNA-encoding RNA can be delivered, e.g., by microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, or a combination thereof. Cas9-encoding and/or gRNA-encoding RNA can be conjugated to molecules (e.g., GalNAc) promoting uptake by the target cells (e.g., target cells described herein).

Delivery Cas9 Protein

Cas9 molecules (e.g., eaCas9 molecules) can be delivered into cells by art-known methods or as described herein. For example, Cas9 protein molecules can be delivered, e.g., by microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, or a combination thereof. Delivery can be accompanied by DNA encoding a gRNA or by a gRNA. Cas9-encoding and/or gRNA-encoding RNA can be conjugated to molecules (e.g., GalNAc) promoting uptake by the target cells (e.g., target cells described herein).

Route of Administration

Systemic modes of administration include oral and parenteral routes. Parenteral routes include, by way of example, intravenous, intrarterial, intramuscular, intradermal, subcutaneous, intranasal and intraperitoneal routes. Components administered systemically may be modified or formulated to target the components to the eye.

Local modes of administration include, by way of example, intraocular, intraorbital, subconjuctival, intravitreal, subretinal or transscleral routes. In an embodiment, significantly smaller amounts of the components (compared with systemic approaches) may exert an effect when administered locally (for example, intravitreally) compared to when administered systemically (for example, intravenously). Local modes of administration can reduce or eliminate the incidence of potentially toxic side effects that may occur when therapeutically effective amounts of a component are administered systemically.

In an embodiment, components described herein are delivered subretinally, e.g., by subretinal injection. Subretinal injections may be made directly into the macular, e.g., submacular injection.

In an embodiment, components described herein are delivered by intravitreal injection. Intravitreal injection has a relatively low risk of retinal detachment. In an embodiment, nanoparticle or viral, e.g., AAV vector, is delivered intravitreally.

Methods for administration of agents to the eye are known in the medical arts and can be used to administer components described herein. Exemplary methods include intraocular injection (e.g., retrobulbar, subretinal, submacular, intravitreal and intrachoridal), iontophoresis, eye drops, and intraocular implantation (e.g., intravitreal, sub-Tenons and sub-conjunctival).

Administration may be provided as a periodic bolus (for example, subretinally, intravenously or intravitreally) or as continuous infusion from an internal reservoir (for example, from an implant disposed at an intra- or extra-ocular location (see, U.S. Pat. Nos. 5,443,505 and 5,766,242)) or from an external reservoir (for example, from an intravenous bag). Components may be administered locally, for example, by continuous release from a sustained release drug delivery device immobilized to an inner wall of the eye or via targeted transscleral controlled release into the choroid (see, e.g., PCT/US00/00207; PCT/US02/14279; Ambati 2000a; Ambati 2000b. A variety of devices suitable for administering components locally to the inside of the eye are known in the art. See, for example, U.S. Pat. Nos. 6,251,090; 6,299,895; 6,416,777; and 6,413,540; and PCT Appl. No. PCT/US00/28187.

In addition, components may be formulated to permit release over a prolonged period of time. A release system can include a matrix of a biodegradable material or a material which releases the incorporated components by diffusion. The components can be homogeneously or heterogeneously distributed within the release system. A variety of release systems may be useful, however, the choice of the appropriate system will depend upon rate of release required by a particular application. Both non-degradable and degradable release systems can be used. Suitable release systems include polymers and polymeric matrices, non-polymeric matrices, or inorganic and organic excipients and diluents such as, but not limited to, calcium carbonate and sugar (for example, trehalose). Release systems may be natural or synthetic. However, synthetic release systems are preferred because generally they are more reliable, more reproducible and produce more defined release profiles. The release system material can be selected so that components having different molecular weights are released by diffusion through or degradation of the material.

Representative synthetic, biodegradable polymers include, for example: polyamides such as poly(amino acids) and poly(peptides); polyesters such as poly(lactic acid), poly(glycolic acid), poly(lactic-co-glycolic acid), and poly(caprolactone); poly(anhydrides); polyorthoesters; polycarbonates; and chemical derivatives thereof (substitutions, additions of chemical groups, for example, alkyl, alkylene, hydroxylations, oxidations, and other modifications routinely made by those skilled in the art), copolymers and mixtures thereof. Representative synthetic, non-degradable polymers include, for example: polyethers such as poly(ethylene oxide), poly(ethylene glycol), and poly(tetramethylene oxide); vinyl polymers-polyacrylates and polymethacrylates such as methyl, ethyl, other alkyl, hydroxyethyl methacrylate, acrylic and methacrylic acids, and others such as poly(vinyl alcohol), poly(vinyl pyrolidone), and poly(vinyl acetate); poly(urethanes); cellulose and its derivatives such as alkyl, hydroxyalkyl, ethers, esters, nitrocellulose, and various cellulose acetates; polysiloxanes; and any chemical derivatives thereof (substitutions, additions of chemical groups, for example, alkyl, alkylene, hydroxylations, oxidations, and other modifications routinely made by those skilled in the art), copolymers and mixtures thereof.

Poly(lactide-co-glycolide) microsphere can also be used for intraocular injection. Typically the microspheres are composed of a polymer of lactic acid and glycolic acid, which are structured to form hollow spheres. The spheres can be approximately 15-30 microns in diameter and can be loaded with components described herein.

Bi-Modal or Differential Delivery of Components

Separate delivery of the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component, and more particularly, delivery of the components by differing modes, can enhance performance, e.g., by improving tissue specificity and safety.

In an embodiment, the Cas9 molecule and the gRNA molecule are delivered by different modes, or as sometimes referred to herein as differential modes. Different or differential modes, as used herein, refer modes of delivery that confer different pharmacodynamic or pharmacokinetic properties on the subject component molecule, e.g., a Cas9 molecule, gRNA molecule, template nucleic acid, or payload. For example, the modes of delivery can result in different tissue distribution, different half-life, or different temporal distribution, e.g., in a selected compartment, tissue, or organ.

Some modes of delivery, e.g., delivery by a nucleic acid vector that persists in a cell, or in progeny of a cell, e.g., by autonomous replication or insertion into cellular nucleic acid, result in more persistent expression of and presence of a component. Examples include viral, e.g., adeno associated virus or lentivirus, delivery.

By way of example, the components, e.g., a Cas9 molecule and a gRNA molecule, can be delivered by modes that differ in terms of resulting half-life or persistent of the delivered component the body, or in a particular compartment, tissue or organ. In an embodiment, a gRNA molecule can be delivered by such modes. The Cas9 molecule component can be delivered by a mode which results in less persistence or less exposure to the body or a particular compartment or tissue or organ.

More generally, in an embodiment, a first mode of delivery is used to deliver a first component and a second mode of delivery is used to deliver a second component. The first mode of delivery confers a first pharmacodynamic or pharmacokinetic property. The first pharmacodynamic property can be, e.g., distribution, persistence, or exposure, of the component, or of a nucleic acid that encodes the component, in the body, a compartment, tissue or organ. The second mode of delivery confers a second pharmacodynamic or pharmacokinetic property. The second pharmacodynamic property can be, e.g., distribution, persistence, or exposure, of the component, or of a nucleic acid that encodes the component, in the body, a compartment, tissue or organ.

In an embodiment, the first pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure, is more limited than the second pharmacodynamic or pharmacokinetic property.

In an embodiment, the first mode of delivery is selected to optimize, e.g., minimize, a pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure.

In an embodiment, the second mode of delivery is selected to optimize, e.g., maximize, a pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure.

In an embodiment, the first mode of delivery comprises the use of a relatively persistent element, e.g., a nucleic acid, e.g., a plasmid or viral vector, e.g., an AAV or lentivirus. As such vectors are relatively persistent product transcribed from them would be relatively persistent.

In an embodiment, the second mode of delivery comprises a relatively transient element, e.g., an RNA or protein.

In an embodiment, the first component comprises gRNA, and the delivery mode is relatively persistent, e.g., the gRNA is transcribed from a plasmid or viral vector, e.g., an AAV or lentivirus. Transcription of these genes would be of little physiological consequence because the genes do not encode for a protein product, and the gRNAs are incapable of acting in isolation. The second component, a Cas9 molecule, is delivered in a transient manner, for example as mRNA or as protein, ensuring that the full Cas9 molecule/gRNA molecule complex is only present and active for a short period of time.

Furthermore, the components can be delivered in different molecular form or with different delivery vectors that complement one another to enhance safety and tissue specificity.

Use of differential delivery modes can enhance performance, safety and efficacy. E.g., the likelihood of an eventual off-target modification can be reduced. Delivery of immunogenic components, e.g., Cas9 molecules, by less persistent modes can reduce immunogenicity, as peptides from the bacterially-derived Cas enzyme are displayed on the surface of the cell by MHC molecules. A two-part delivery system can alleviate these drawbacks.

Differential delivery modes can be used to deliver components to different, but overlapping target regions. The formation active complex is minimized outside the overlap of the target regions. Thus, in an embodiment, a first component, e.g., a gRNA molecule is delivered by a first delivery mode that results in a first spatial, e.g., tissue, distribution. A second component, e.g., a Cas9 molecule is delivered by a second delivery mode that results in a second spatial, e.g., tissue, distribution. In an embodiment the first mode comprises a first element selected from a liposome, nanoparticle, e.g., polymeric nanoparticle, and a nucleic acid, e.g., viral vector. The second mode comprises a second element selected from the group. In an embodiment, the first mode of delivery comprises a first targeting element, e.g., a cell specific receptor or an antibody, and the second mode of delivery does not include that element. In embodiment, the second mode of delivery comprises a second targeting element, e.g., a second cell specific receptor or second antibody.

When the Cas9 molecule is delivered in a virus delivery vector, a liposome, or polymeric nanoparticle, there is the potential for delivery to and therapeutic activity in multiple tissues, when it may be desirable to only target a single tissue. A two-part delivery system can resolve this challenge and enhance tissue specificity. If the gRNA molecule and the Cas9 molecule are packaged in separated delivery vehicles with distinct but overlapping tissue tropism, the fully functional complex is only be formed in the tissue that is targeted by both vectors.

Ex Vivo Delivery

In some embodiments, components described in Table 18 are introduced into cells which are then introduced into the subject. Methods of introducing the components can include, e.g., any of the delivery methods described in Table 19.

VIII. Modified Nucleosides, Nucleotides, and Nucleic Acids

Modified nucleosides and modified nucleotides can be present in nucleic acids, e.g., particularly gRNA, but also other forms of RNA, e.g., mRNA, RNAi, or siRNA. As described herein, “nucleoside” is defined as a compound containing a five-carbon sugar molecule (a pentose or ribose) or derivative thereof, and an organic base, purine or pyrimidine, or a derivative thereof. As described herein, “nucleotide” is defined as a nucleoside further comprising a phosphate group.

Modified nucleosides and nucleotides can include one or more of:

(i) alteration, e.g., replacement, of one or both of the non-linking phosphate oxygens and/or of one or more of the linking phosphate oxygens in the phosphodiester backbone linkage;

(ii) alteration, e.g., replacement, of a constituent of the ribose sugar, e.g., of the 2′ hydroxyl on the ribose sugar;

(iii) wholesale replacement of the phosphate moiety with “dephospho” linkers;

(iv) modification or replacement of a naturally occurring nucleobase;

(v) replacement or modification of the ribose-phosphate backbone;

(vi) modification of the 3′ end or 5′ end of the oligonucleotide, e.g., removal, modification or replacement of a terminal phosphate group or conjugation of a moiety; and

(vii) modification of the sugar.

The modifications listed above can be combined to provide modified nucleosides and nucleotides that can have two, three, four, or more modifications. For example, a modified nucleoside or nucleotide can have a modified sugar and a modified nucleobase. In an embodiment, every base of a gRNA is modified, e.g., all bases have a modified phosphate group, e.g., all are phosphorothioate groups. In an embodiment, all, or substantially all, of the phosphate groups of a unimolecular or modular gRNA molecule are replaced with phosphorothioate groups.

In an embodiment, modified nucleotides, e.g., nucleotides having modifications as described herein, can be incorporated into a nucleic acid, e.g., a “modified nucleic acid.” In some embodiments, the modified nucleic acids comprise one, two, three or more modified nucleotides. In some embodiments, at least 5% (e.g., at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100%) of the positions in a modified nucleic acid are a modified nucleotides.

Unmodified nucleic acids can be prone to degradation by, e.g., cellular nucleases. For example, nucleases can hydrolyze nucleic acid phosphodiester bonds. Accordingly, in one aspect the modified nucleic acids described herein can contain one or more modified nucleosides or nucleotides, e.g., to introduce stability toward nucleases.

In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can exhibit a reduced innate immune response when introduced into a population of cells, both in vivo and ex vivo. The term “innate immune response” includes a cellular response to exogenous nucleic acids, including single stranded nucleic acids, generally of viral or bacterial origin, which involves the induction of cytokine expression and release, particularly the interferons, and cell death. In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can disrupt binding of a major groove interacting partner with the nucleic acid. In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can exhibit a reduced innate immune response when introduced into a population of cells, both in vivo and ex vivo, and also disrupt binding of a major groove interacting partner with the nucleic acid.

Definitions of Chemical Groups

As used herein, “alkyl” is meant to refer to a saturated hydrocarbon group which is straight-chained or branched. Example alkyl groups include methyl (Me), ethyl (Et), propyl (e.g., n-propyl and isopropyl), butyl (e.g., n-butyl, isobutyl, t-butyl), pentyl (e.g., n-pentyl, isopentyl, neopentyl), and the like. An alkyl group can contain from 1 to about 20, from 2 to about 20, from 1 to about 12, from 1 to about 8, from 1 to about 6, from 1 to about 4, or from 1 to about 3 carbon atoms.

As used herein, “aryl” refers to monocyclic or polycyclic (e.g., having 2, 3 or 4 fused rings) aromatic hydrocarbons such as, for example, phenyl, naphthyl, anthracenyl, phenanthrenyl, indanyl, indenyl, and the like. In some embodiments, aryl groups have from 6 to about 20 carbon atoms.

As used herein, “alkenyl” refers to an aliphatic group containing at least one double bond.

As used herein, “alkynyl” refers to a straight or branched hydrocarbon chain containing 2-12 carbon atoms and characterized in having one or more triple bonds. Examples of alkynyl groups include, but are not limited to, ethynyl, propargyl, and 3-hexynyl.

As used herein, “arylalkyl” or “aralkyl” refers to an alkyl moiety in which an alkyl hydrogen atom is replaced by an aryl group. Aralkyl includes groups in which more than one hydrogen atom has been replaced by an aryl group. Examples of “arylalkyl” or “aralkyl” include benzyl, 2-phenylethyl, 3-phenylpropyl, 9-fluorenyl, benzhydryl, and trityl groups.

As used herein, “cycloalkyl” refers to a cyclic, bicyclic, tricyclic, or polycyclic non-aromatic hydrocarbon groups having 3 to 12 carbons. Examples of cycloalkyl moieties include, but are not limited to, cyclopropyl, cyclopentyl, and cyclohexyl.

As used herein, “heterocyclyl” refers to a monovalent radical of a heterocyclic ring system. Representative heterocyclyls include, without limitation, tetrahydrofuranyl, tetrahydrothienyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, and morpholinyl.

As used herein, “heteroaryl” refers to a monovalent radical of a heteroaromatic ring system. Examples of heteroaryl moieties include, but are not limited to, imidazolyl, oxazolyl, thiazolyl, triazolyl, pyrrolyl, furanyl, indolyl, thiophenyl pyrazolyl, pyridinyl, pyrazinyl, pyridazinyl, pyrimidinyl, indolizinyl, purinyl, naphthyridinyl, quinolyl, and pteridinyl.

Phosphate Backbone Modifications Phosphate Group

In some embodiments, the phosphate group of a modified nucleotide can be modified by replacing one or more of the oxygens with a different substituent. Further, the modified nucleotide, e.g., modified nucleotide present in a modified nucleic acid, can include the wholesale replacement of an unmodified phosphate moiety with a modified phosphate as described herein. In some embodiments, the modification of the phosphate backbone can include alterations that result in either an uncharged linker or a charged linker with unsymmetrical charge distribution.

Examples of modified phosphate groups include, phosphorothioate, phosphoroselenates, borano phosphates, borano phosphate esters, hydrogen phosphonates, phosphoroamidates, alkyl or aryl phosphonates and phosphotriesters. In some embodiments, one of the non-bridging phosphate oxygen atoms in the phosphate backbone moiety can be replaced by any of the following groups: sulfur (S), selenium (Se), BR₃ (wherein R can be, e.g., hydrogen, alkyl, or aryl), C (e.g., an alkyl group, an aryl group, and the like), H, NR₂ (wherein R can be, e.g., hydrogen, alkyl, or aryl), or OR (wherein R can be, e.g., alkyl or aryl). The phosphorous atom in an unmodified phosphate group is achiral. However, replacement of one of the non-bridging oxygens with one of the above atoms or groups of atoms can render the phosphorous atom chiral; that is to say that a phosphorous atom in a phosphate group modified in this way is a stereogenic center. The stereogenic phosphorous atom can possess either the “R” configuration (herein Rp) or the “S” configuration (herein Sp).

Phosphorodithioates have both non-bridging oxygens replaced by sulfur. The phosphorus center in the phosphorodithioates is achiral which precludes the formation of oligoribonucleotide diastereomers. In some embodiments, modifications to one or both non-bridging oxygens can also include the replacement of the non-bridging oxygens with a group independently selected from S, Se, B, C, H, N, and OR (R can be, e.g., alkyl or aryl).

The phosphate linker can also be modified by replacement of a bridging oxygen, (i.e., the oxygen that links the phosphate to the nucleoside), with nitrogen (bridged phosphoroamidates), sulfur (bridged phosphorothioates) and carbon (bridged methylenephosphonates). The replacement can occur at either linking oxygen or at both of the linking oxygens.

Replacement of the Phosphate Group

The phosphate group can be replaced by non-phosphorus containing connectors. In some embodiments, the charge phosphate group can be replaced by a neutral moiety.

Examples of moieties which can replace the phosphate group can include, without limitation, e.g., methyl phosphonate, hydroxylamino, siloxane, carbonate, carboxymethyl, carbamate, amide, thioether, ethylene oxide linker, sulfonate, sulfonamide, thioformacetal, formacetal, oxime, methyleneimino, methylenemethylimino, methylenehydrazo, methylenedimethylhydrazo and methyleneoxymethylimino.

Replacement of the Ribophosphate Backbone

Scaffolds that can mimic nucleic acids can also be constructed wherein the phosphate linker and ribose sugar are replaced by nuclease resistant nucleoside or nucleotide surrogates. In some embodiments, the nucleobases can be tethered by a surrogate backbone. Examples can include, without limitation, the morpholino, cyclobutyl, pyrrolidine and peptide nucleic acid (PNA) nucleoside surrogates.

Sugar Modifications

The modified nucleosides and modified nucleotides can include one or more modifications to the sugar group. For example, the 2′ hydroxyl group (OH) can be modified or replaced with a number of different “oxy” or “deoxy” substituents. In some embodiments, modifications to the 2′ hydroxyl group can enhance the stability of the nucleic acid since the hydroxyl can no longer be deprotonated to form a 2′-alkoxide ion. The 2′-alkoxide can catalyze degradation by intramolecular nucleophilic attack on the linker phosphorus atom.

Examples of “oxy”-2′ hydroxyl group modifications can include alkoxy or aryloxy (OR, wherein “R” can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or a sugar); polyethyleneglycols (PEG), O(CH₂CH₂O)_(n)CH₂CH₂OR wherein R can be, e.g., H or optionally substituted alkyl, and n can be an integer from 0 to 20 (e.g., from 0 to 4, from 0 to 8, from 0 to 10, from 0 to 16, from 1 to 4, from 1 to 8, from 1 to 10, from 1 to 16, from 1 to 20, from 2 to 4, from 2 to 8, from 2 to 10, from 2 to 16, from 2 to 20, from 4 to 8, from 4 to 10, from 4 to 16, and from 4 to 20). In some embodiments, the “oxy”-2′ hydroxyl group modification can include “locked” nucleic acids (LNA) in which the 2′ hydroxyl can be connected, e.g., by a C₁₋₆ alkylene or C₁₋₆ heteroalkylene bridge, to the 4′ carbon of the same ribose sugar, where exemplary bridges can include methylene, propylene, ether, or amino bridges; O-amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, or diheteroarylamino, ethylenediamine, or polyamino) and aminoalkoxy, O(CH₂)_(n)-amino, (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, or diheteroarylamino, ethylenediamine, or polyamino). In some embodiments, the “oxy”-2′ hydroxyl group modification can include the methoxyethyl group (MOE), (OCH₂CH₂OCH₃, e.g., a PEG derivative).

“Deoxy” modifications can include hydrogen (i.e. deoxyribose sugars, e.g., at the overhang portions of partially ds RNA); halo (e.g., bromo, chloro, fluoro, or iodo); amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, diheteroarylamino, or amino acid); NH(CH₂CH₂NH)_(n)CH₂CH₂-amino (wherein amino can be, e.g., as described herein), —NHC(O)R (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), cyano; mercapto; alkyl-thio-alkyl; thioalkoxy; and alkyl, cycloalkyl, aryl, alkenyl and alkynyl, which may be optionally substituted with e.g., an amino as described herein.

The sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose. Thus, a modified nucleic acid can include nucleotides containing e.g., arabinose, as the sugar. The nucleotide “monomer” can have an alpha linkage at the 1′ position on the sugar, e.g., alpha-nucleosides.

The modified nucleic acids can also include “abasic” sugars, which lack a nucleobase at C-1′. These abasic sugars can also be further modified at one or more of the constituent sugar atoms. The modified nucleic acids can also include one or more sugars that are in the L form, e.g. L-nucleosides.

Generally, RNA includes the sugar group ribose, which is a 5-membered ring having an oxygen. Exemplary modified nucleosides and modified nucleotides can include, without limitation, replacement of the oxygen in ribose (e.g., with sulfur (S), selenium (Se), or alkylene, such as, e.g., methylene or ethylene); addition of a double bond (e.g., to replace ribose with cyclopentenyl or cyclohexenyl); ring contraction of ribose (e.g., to form a 4-membered ring of cyclobutane or oxetane); ring expansion of ribose (e.g., to form a 6- or 7-membered ring having an additional carbon or heteroatom, such as for example, anhydrohexitol, altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has a phosphoramidate backbone). In some embodiments, the modified nucleotides can include multicyclic forms (e.g., tricyclo; and “unlocked” forms, such as glycol nucleic acid (GNA) (e.g., R-GNA or S-GNA, where ribose is replaced by glycol units attached to phosphodiester bonds), threose nucleic acid (TNA, where ribose is replaced with α-L-threofuranosyl-(3→2′)).

Modifications on the Nucleobase

The modified nucleosides and modified nucleotides described herein, which can be incorporated into a modified nucleic acid, can include a modified nucleobase. Examples of nucleobases include, but are not limited to, adenine (A), guanine (G), cytosine (C), and uracil (U). These nucleobases can be modified or wholly replaced to provide modified nucleosides and modified nucleotides that can be incorporated into modified nucleic acids. The nucleobase of the nucleotide can be independently selected from a purine, a pyrimidine, a purine or pyrimidine analog. In some embodiments, the nucleobase can include, for example, naturally-occurring and synthetic derivatives of a base.

Uracil

In some embodiments, the modified nucleobase is a modified uracil. Exemplary nucleobases and nucleosides having a modified uracil include without limitation pseudouridine (ψ), pyridin-4-one ribonucleoside, 5-aza-uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine (s2U), 4-thio-uridine (s4U), 4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxy-uridine (ho⁵U), 5-aminoallyl-uridine, 5-halo-uridine (e.g., 5-iodo-uridine or 5-bromo-uridine), 3-methyl-uridine (m³U), 5-methoxy-uridine (mo⁵U), uridine 5-oxyacetic acid (cmo⁵U), uridine 5-oxyacetic acid methyl ester (mcmo⁵U), 5-carboxymethyl-uridine (cm⁵U), 1-carboxymethyl-pseudouridine, 5-carboxyhydroxymethyl-uridine (chm⁵U), 5-carboxyhydroxymethyl-uridine methyl ester (mchm⁵U), 5-methoxycarbonylmethyl-uridine (mcm⁵U), 5-methoxycarbonylmethyl-2-thio-uridine (mcm⁵s2U), 5-aminomethyl-2-thio-uridine (nm⁵s2U), 5-methylaminomethyl-uridine (mnm⁵U), 5-methylaminomethyl-2-thio-uridine (mnm⁵s2U), 5-methylaminomethyl-2-seleno-uridine (mnm⁵se²U), 5-carbamoylmethyl-uridine (ncm⁵U), 5-carboxymethylaminomethyl-uridine (cmnm⁵U), 5-carboxymethylaminomethyl-2-thio-uridine (cmnm ⁵s2U), 5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyl-uridine (τcm⁵U), 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine(τm⁵s2U), 1-taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine (m⁵U, i.e., having the nucleobase deoxythymine), 1-methyl-pseudouridine (m¹ψ), 5-methyl-2-thio-uridine (m⁵s2U), 1-methyl-4-thio-pseudouridine (m¹s⁴ψ), 4-thio-1-methyl-pseudouridine, 3-methyl-pseudouridine (m³ψ), 2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine (D), dihydropseudouridine, 5,6-dihydrouridine, 5-methyl-dihydrouridine (m⁵D), 2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxy-uridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2-thio-pseudouridine, N1-methyl-pseudouridine, 3 -(3 -amino-3 -carboxypropyl)uridine (acp³U), 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine (acp³ψ), 5-(isopentenylaminomethyl)uridine (inm⁵U), 5-(isopentenylaminomethyl)-2-thio-uridine (inm⁵s2U), α-thio-uridine, 2′-O-methyl-uridine (Um), 5,2′-O-dimethyl-uridine (m⁵Um), 2′-O-methyl-pseudouridine (ψm), 2-thio-2′-O-methyl-uridine (s2Um), 5-methoxycarbonylmethyl-2′-O-methyl-uridine (mcm⁵Um), 5-carbamoylmethyl-2′-O-methyl-uridine (ncm⁵Um), 5-carboxymethylaminomethyl-2′-O-methyl-uridine (cmnm⁵Um), 3,2′-O-dimethyl-uridine (m³Um), 5-(isopentenylaminomethyl)-2′-O-methyl-uridine (inm ⁵Um), 1-thio-uridine, deoxythymidine, 2′-F-ara-uridine, 2′-F-uridine, 2′-OH-ara-uridine, 5-(2-carbomethoxyvinyl) uridine, 5-[3-(1-E-propenylamino)uridine, pyrazolo[3,4-d]pyrimidines, xanthine, and hypoxanthine.

Cytosine

In some embodiments, the modified nucleobase is a modified cytosine. Exemplary nucleobases and nucleosides having a modified cytosine include without limitation 5-aza-cytidine, 6-aza-cytidine, pseudoisocytidine, 3-methyl-cytidine (m³C), N4-acetyl-cytidine (act), 5-formyl-cytidine (f⁵C), N4-methyl-cytidine (m⁴C), 5-methyl-cytidine (m⁵C), 5-halo-cytidine (e.g., 5-iodo-cytidine), 5-hydroxymethyl-cytidine (hm⁵C), 1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine (s2C), 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1-methyl-1-deaza-pseudoisocytidine, 1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, lysidine (k²C), α-thio-cytidine, 2′-O-methyl-cytidine (Cm), 5,2′-O-dimethyl-cytidine (m⁵Cm), N4-acetyl-2′-O-methyl-cytidine (ac⁴Cm), N4,2′-O-dimethyl-cytidine (m⁴Cm), 5-formyl-2′-O-methyl-cytidine (f⁵Cm), N4,N4,2′-O-trimethyl-cytidine (m⁴2Cm), 1-thio-cytidine, 2′-F-ara-cytidine, 2′-F-cytidine, and 2′-OH-ara-cytidine.

Adenine

In some embodiments, the modified nucleobase is a modified adenine. Exemplary nucleobases and nucleosides having a modified adenine include without limitation 2-amino-purine, 2,6-diaminopurine, 2-amino-6-halo-purine (e.g., 2-amino-6-chloro-purine), 6-halo-purine (e.g., 6-chloro-purine), 2-amino-6-methyl-purine, 8-azido-adenosine, 7-deaza-adenine, 7-deaza-8-aza-adenine, 7-deaza-2-amino-purine, 7-deaza-8-aza-2-amino-purine, 7-deaza-2,6-diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1-methyl-adenosine (m¹A), 2-methyl-adenine (m²A), N6-methyl-adenosine (m⁶A), 2-methylthio-N6-methyl-adenosine (ms2m⁶A), N6-isopentenyl-adenosine (i⁶A), 2-methylthio-N6-isopentenyl-adenosine (ms²i⁶A), N6-(cis-hydroxyisopentenyl)adenosine (io⁶A), 2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine (ms2io⁶A), N6-glycinylcarbamoyl-adenosine (g⁶A), N6-threonylcarbamoyl-adenosine (t⁶A), N6-methyl-N6-threonylcarbamoyl-adenosine (m⁶t⁶A), 2-methylthio-N6-threonylcarbamoyl-adenosine (ms²g⁶A), N6,N6-dimethyl-adenosine (m⁶ ₂A), N6-hydroxynorvalylcarbamoyl-adenosine (hn⁶A), 2-methylthio-N6-hydroxynorvalylcarbamoyl-adenosine (ms2hn⁶A), N6-acetyl-adenosine (ac⁶A), 7-methyl-adenine, 2-methylthio-adenine, 2-methoxy-adenine, α-thio-adenosine, 2′-O-methyl-adenosine (Am), N⁶,2′-O-dimethyl-adenosine (m⁶Am), N⁶-Methyl-2′-deoxyadenosine, N6,N6,2′-O-trimethyl-adenosine (m⁶ ₂Am), 1,2′-O-dimethyl-adenosine (m¹Am), 2′-O-ribosyladenosine (phosphate) (Ar(p)), 2-amino-N6-methyl-purine, 1-thio-adenosine, 8-azido-adenosine, 2′-F-ara-adenosine, 2′-F-adenosine, 2′-OH-ara-adenosine, and N6-(19-amino-pentaoxanonadecyl)-adenosine.

Guanine

In some embodiments, the modified nucleobase is a modified guanine. Exemplary nucleobases and nucleosides having a modified guanine include without limitation inosine (I), 1-methyl-inosine (m¹I), wyosine (imG), methylwyosine (mimG), 4-demethyl-wyosine (imG-14), isowyosine (imG2), wybutosine (yW), peroxywybutosine (o₂yW), hydroxywybutosine (OHyW), undermodified hydroxywybutosine (OHyW*), 7-deaza-guanosine, queuosine (Q), epoxyqueuosine (oQ), galactosyl-queuosine (galQ), mannosyl-queuosine (manQ), 7-cyano-7-deaza-guanosine (preQ₀), 7-aminomethyl-7-deaza-guanosine (preQ₁), archaeosine (G⁺), 7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine (m⁷G), 6-thio-7-methyl-guanosine, 7-methyl-inosine, 6-methoxy-guanosine, 1-methyl-guanosine (m′G), N2-methyl-guanosine (m²G), N2,N2-dimethyl-guanosine (m² ₂G), N2,7-dimethyl-guanosine (m²,7G), N2, N2,7-dimethyl-guanosine (m²,2,7G), 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-meth thio-guanosine, N2-methyl-6-thio-guanosine, N2,N2-dimethyl-6-thio-guanosine, α-thio-guanosine, 2′-O-methyl-guanosine (Gm), N2-methyl-2′-O-methyl-guanosine (m²Gm), N2,N2-dimethyl-2′-O-methyl-guanosine (m² ₂Gm), 1-methyl-2′-O-methyl-guanosine (m′Gm), N2,7-dimethyl-2′-O-methyl-guanosine (m²,7Gm), 2′-O-methyl-inosine (Im), 1,2′-O-dimethyl-inosine (m′Im), O⁶-phenyl-2′-deoxyinosine, 2′-O-ribosylguanosine (phosphate) (Gr(p)), 1-thio-guanosine, O⁶-methyl-guanosine, O⁶-Methyl-2′-deoxyguanosine, 2′-F-ara-guanosine, and 2′-F-guanosine.

Modified gRNAs

In some embodiments, the modified nucleic acids can be modified gRNAs. In some embodiments, gRNAs can be modified at the 3′ end. In this embodiment, the gRNAs can be modified at the 3′ terminal U ribose. For example, the two terminal hydroxyl groups of the U ribose can be oxidized to aldehyde groups and a concomitant opening of the ribose ring to afford a modified nucleoside as sown below:

wherein “U” can be an unmodified or modified uridine.

In another embodiment, the 3′ terminal U can be modified with a 2′3′ cyclic phosphate as shown below:

wherein “U” can be an unmodified or modified uridine.

In some embodiments, the gRNA molecules may contain 3′ nucleotides which can be stabilized against degradation, e.g., by incorporating one or more of the modified nucleotides described herein. In this embodiment, e.g., uridines can be replaced with modified uridines, e.g., 5-(2-amino)propyl uridine, and 5-bromo uridine, or with any of the modified uridines described herein; adenosines and guanosines can be replaced with modified adenosines and guanosines, e.g., with modifications at the 8-position, e.g., 8-bromo guanosine, or with any of the modified adenosines or guanosines described herein. In some embodiments, deaza nucleotides, e.g., 7-deaza-adenosine, can be incorporated into the gRNA. In some embodiments, O- and N-alkylated nucleotides, e.g., N6-methyl adenosine, can be incorporated into the gRNA. In some embodiments, sugar-modified ribonucleotides can be incorporated, e.g., wherein the 2′ OH-group is replaced by a group selected from H, —OR, —R (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), halo, —SH, —SR (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, diheteroarylamino, or amino acid); or cyano (—CN). In some embodiments, the phosphate backbone can be modified as described herein, e.g., with a phosphothioate group. In some embodiments, the nucleotides in the overhang region of the gRNA can each independently be a modified or unmodified nucleotide including, but not limited to 2′-sugar modified, such as, 2-F 2′-O-methyl, thymidine (T), 2′-O-methoxyethyl-5-methyluridine (Teo), 2′-O-methoxyethyladenosine (Aeo), 2′-O-methoxyethyl-5-methylcytidine (m5Ceo), and any combinations thereof.

In an embodiment, one or more or all of the nucleotides in single stranded RNA molecule, e.g., a gRNA molecule, are deoxynucleotides.

miRNA Binding Sites

microRNAs (or miRNAs) are naturally occurring cellular 19-25 nucleotide long noncoding RNAs. They bind to nucleic acid molecules having an appropriate miRNA binding site, e.g., in the 3′ UTR of an mRNA, and down-regulate gene expression. While not wishing to be bound by theory, in an embodiment, it is believed that the down regulation is either by reducing nucleic acid molecule stability or by inhibiting translation. An RNA species disclosed herein, e.g., an mRNA encoding Cas9 can comprise an miRNA binding site, e.g., in its 3′UTR. The miRNA binding site can be selected to promote down regulation of expression is a selected cell type. By way of example, the incorporation of a binding site for miR-122, a microRNA abundant in liver, can inhibit the expression of the gene of interest in the liver.

Governing gRNA Molecules and the Use Thereof to Limit the Activity of a Cas9 System

Methods and compositions that use, or include, a nucleic acid, e.g., DNA, that encodes a Cas9 molecule or a gRNA molecule, can, in addition, use or include a “governing gRNA molecule.” The governing gRNA can limit the activity of the other CRISPR/Cas components introduced into a cell or subject. In an embodiment, a gRNA molecule comprises a targeting domain that is complementary to a target domain on a nucleic acid that comprises a sequence that encodes a component of the CRISPR/Cas system that is introduced into a cell or subject. In an embodiment, a governing gRNA molecule comprises a targeting domain that is complementary with a target sequence on: (a) a nucleic acid that encodes a Cas9 molecule; (b) a nucleic acid that encodes a gRNA which comprises a targeting domain that targets the CEP290 gene (a target gene gRNA); or on more than one nucleic acid that encodes a CRISPR/Cas component, e.g., both (a) and (b). The governing gRNA molecule can complex with the Cas9 molecule to inactivate a component of the system. In an embodiment, a Cas9 molecule/governing gRNA molecule complex inactivates a nucleic acid that comprises the sequence encoding the Cas9 molecule. In an embodiment, a Cas9 molecule/governing gRNA molecule complex inactivates the nucleic acid that comprises the sequence encoding a target gene gRNA molecule. In an embodiment, a Cas9 molecule/governing gRNA molecule complex places temporal, level of expression, or other limits, on activity of the Cas9 molecule/target gene gRNA molecule complex. In an embodiment, a Cas9 molecule/governing gRNA molecule complex reduces off-target or other unwanted activity. In an embodiment, a governing gRNA molecule targets the coding sequence, or a control region, e.g., a promoter, for the CRISPR/Cas system component to be negatively regulated. For example, a governing gRNA can target the coding sequence for a Cas9 molecule, or a control region, e.g., a promoter, that regulates the expression of the Cas9 molecule coding sequence, or a sequence disposed between the two. In an embodiment, a governing gRNA molecule targets the coding sequence, or a control region, e.g., a promoter, for a target gene gRNA. In an embodiment, a governing gRNA, e.g., a Cas9-targeting or target gene gRNA-targeting, governing gRNA molecule, or a nucleic acid that encodes it, is introduced separately, e.g., later, than is the Cas9 molecule or a nucleic acid that encodes it. For example, a first vector, e.g., a viral vector, e.g., an AAV vector, can introduce nucleic acid encoding a Cas9 molecule and one or more target gene gRNA molecules, and a second vector, e.g., a viral vector, e.g., an AAV vector, can introduce nucleic acid encoding a governing gRNA molecule, e.g., a Cas9-targeting or target gene gRNA targeting, gRNA molecule. In an embodiment, the second vector can be introduced after the first. In other embodiments, a governing gRNA molecule, e.g., a Cas9-targeting or target gene gRNA targeting, governing gRNA molecule, or a nucleic acid that encodes it, can be introduced together, e.g., at the same time or in the same vector, with the Cas9 molecule or a nucleic acid that encodes it, but, e.g., under transcriptional control elements, e.g., a promoter or an enhancer, that are activated at a later time, e.g., such that after a period of time the transcription of Cas9 is reduced. In an embodiment, the transcriptional control element is activated intrinsically. In an embodiment, the transcriptional element is activated via the introduction of an external trigger.

Typically a nucleic acid sequence encoding a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule, is under the control of a different control region, e.g., promoter, than is the component it negatively modulates, e.g., a nucleic acid encoding a Cas9 molecule. In an embodiment, “different control region” refers to simply not being under the control of one control region, e.g., promoter, that is functionally coupled to both controlled sequences. In an embodiment, different refers to “different control region” in kind or type of control region. For example, the sequence encoding a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule, is under the control of a control region, e.g., a promoter, that has a lower level of expression, or is expressed later than the sequence which encodes is the component it negatively modulates, e.g., a nucleic acid encoding a Cas9 molecule.

By way of example, a sequence that encodes a governing gRNA molecule, e.g., a Cas9-targeting governing gRNA molecule, can be under the control of a control region (e.g., a promoter) described herein, e.g., human U6 small nuclear promoter, or human H1 promoter. In an embodiment, a sequence that encodes the component it negatively regulates, e.g., a nucleic acid encoding a Cas9 molecule, can be under the control of a control region (e.g., a promoter) described herein, e.g., CMV, EF-1a, MSCV, PGK, CAG control promoters.

EXAMPLES

The following Examples are merely illustrative and are not intended to limit the scope or content of the invention in any way.

Example 1 Cloning and Initial Screening of gRNAs

The suitability of candidate gRNAs can be evaluated as described in this example. Although described for a chimeric gRNA, the approach can also be used to evaluate modular gRNAs.

Cloning gRNAs into Plasmid Vector

For each gRNA, a pair of overlapping oligonucleotides is designed and obtained. Oligonucleotides are annealed and ligated into a digested vector backbone containing an upstream U6 promoter and the remaining sequence of a long chimeric gRNA. Plasmid is sequence-verified and prepped to generate sufficient amounts of transfection-quality DNA. Alternate promoters maybe used to drive in vivo transcription (e.g., H1 promoter) or for in vitro transcription (e.g., T7 promoter).

Cloning gRNAs in Linear dsDNA Molecule (STITCHR)

For each gRNA, a single oligonucleotide is designed and obtained. The U6 promoter and the gRNA scaffold (e.g. including everything except the targeting domain, e.g., including sequences derived from the crRNA and tracrRNA, e.g., including a first complementarity domain; a linking domain; a second complementarity domain; a proximal domain; and a tail domain) are separately PCR amplified and purified as dsDNA molecules. The gRNA-specific oligonucleotide is used in a PCR reaction to stitch together the U6 and the gRNA scaffold, linked by the targeting domain specified in the oligonucleotide. Resulting dsDNA molecule (STITCHR product) is purified for transfection. Alternate promoters may be used to drive in vivo transcription (e.g., H1 promoter) or for in vitro transcription (e.g., T7 promoter). Any gRNA scaffold may be used to create gRNAs compatible with Cas9s from any bacterial species.

Initial gRNA Screen

Each gRNA to be tested is transfected, along with a plasmid expressing Cas9 and a small amount of a GFP-expressing plasmid into human cells. In preliminary experiments, these cells can be immortalized human cell lines such as 293T, K562 or U2OS. Alternatively, primary human cells may be used. In this case, cells may be relevant to the eventual therapeutic cell target (for example, photoreceptor cells). The use of primary cells similar to the potential therapeutic target cell population may provide important information on gene targeting rates in the context of endogenous chromatin and gene expression.

Transfection may be performed using lipid transfection (such as Lipofectamine or Fugene) or by electroporation. Following transfection, GFP expression can be determined either by fluorescence microscopy or by flow cytometry to confirm consistent and high levels of transfection. These preliminary transfections can comprise different gRNAs and different targeting approaches (17-mers, 20-mers, nuclease, dual-nickase, etc.) to determine which gRNAs/combinations of gRNAs give the greatest activity.

Efficiency of cleavage with each gRNA may be assessed by measuring NHEJ-induced indel formation at the target locus by a T7E1-type assay or by sequencing. Alternatively, other mismatch-sensitive enzymes, such as Cell/Surveyor nuclease, may also be used.

For the T7E1 assay, PCR amplicons are approximately 500-700 bp with the intended cut site placed asymmetrically in the amplicon. Following amplification, purification and size-verification of PCR products, DNA is denatured and re-hybridized by heating to 95° C. and then slowly cooling. Hybridized PCR products are then digested with T7 Endonuclease I (or other mismatch-sensitive enzyme) which recognizes and cleaves non-perfectly matched DNA. If indels are present in the original template DNA, when the amplicons are denatured and re-annealed, this results in the hybridization of DNA strands harboring different indels and therefore lead to double-stranded DNA that is not perfectly matched. Digestion products may be visualized by gel electrophoresis or by capillary electrophoresis. The fraction of DNA that is cleaved (density of cleavage products divided by the density of cleaved and uncleaved) may be used to estimate a percent NHEJ using the following equation: % NHEJ=(1−(1−fraction cleaved)^(1/2)). The T7E1 assay is sensitive down to about 2-5% NHEJ.

Sequencing may be used instead of, or in addition to, the T7E1 assay. For Sanger sequencing, purified PCR amplicons are cloned into a plasmid backbone, transformed, miniprepped and sequenced with a single primer. For large sequencing numbers, Sanger sequencing may be used for determining the exact nature of indels after determining the NHEJ rate by T7E1.

Sequencing may also be performed using next generation sequencing techniques. When using next generation sequencing, amplicons may be 300-500 bp with the intended cut site placed asymmetrically. Following PCR, next generation sequencing adapters and barcodes (for example Illumina multiplex adapters and indexes) may be added to the ends of the amplicon, e.g., for use in high throughput sequencing (for example on an Illumina MiSeq). This method allows for detection of very low NHEJ rates.

Example 2 Assessment of Gene Targeting by NHEJ

The gRNAs that induce the greatest levels of NHEJ in initial tests can be selected for further evaluation of gene targeting efficiency. For example, cells may be derived from disease subjects, relevant cell lines, and/or animal models and, therefore, harbor the relevant mutation.

Following transfection (usually 2-3 days post-transfection,) genomic DNA may be isolated from a bulk population of transfected cells and PCR may be used to amplify the target region. Following PCR, gene targeting efficiency to generate the desired mutations (either knockout of a target gene or removal of a target sequence motif) may be determined by sequencing. For Sanger sequencing, PCR amplicons may be 500-700 bp long. For next generation sequencing, PCR amplicons may be 300-500 bp long. If the goal is to knockout gene function, sequencing may be used to assess what percent of alleles have undergone NHEJ-induced indels that result in a frameshift or large deletion or insertion that would be expected to destroy gene function. If the goal is to remove a specific sequence motif, sequencing may be used to assess what percent of alleles have undergone NHEJ-induced deletions that span this sequence.

Example 3 Assessment of Activity of Individual gRNAs Targeting CEP290

Guide RNA were identified using a custom guide RNA design software based on the public tool cas-offinder (Bae 2014). Each gRNA to be tested was generated as a STITCHR product and co-transfected with a plasmid expressing either S. aureus Cas9 (pAF003) or S. pyogenes Cas9 (pJDS246) into either HEK293 cells or primary fibroblasts derived from and LCA10 patient harboring homozygous IVS26 c.2991+1655A to G mutations (hereafter referred to as IVS26 fibroblasts). The pAF003 plasmid encodes the S. aureus Cas9, with N-terminal and C-terminal nuclear localization signals (NLS) and a C-terminal triple flag tag, driven by a CMV promoter. The pJDS246 plasmid encodes the S. pyogenes Cas9, with a C-terminal nuclear localization signal (NLS) and a C-terminal triple flag tag, driven by a CMV promoter. gRNA and Cas9-encoding DNA was introduced into cells by either Mirus TranslT-293 transfection reagent (for 293 cells) or by Amaxa nucleofection (for IVS26 fibroblasts). Nucleofection was optimized for transfection of IVS26 fibroblasts using solution P2 and various pulse codes and assaying for highest levels of gene editing and cell viability. Transfection efficiency in both cell types was assessed by transfecting with GFP and assaying expression by fluorescent microscopy. Three to seven days post-transfection, genomic DNA was isolated from bulk populations of transfected cells and the region of the CEP290 locus surrounding the target site was PCR amplified. PCR amplicons were then cloned into a plasmid backbone using the Zero-Blunt TOPO cloning kit (Life Technologies) and transformed into chemically competent Top10 cells. Bacterial colonies were then cultured and plasmid DNA was isolated and sequenced. Sequencing of PCR products allowed for the detection and quantification of targeted insertion and deletion (indel) events at the target site. FIGS. 11A and 11B show the rates of indels induced by various gRNAs at the CEP290 locus. FIG. 11A shows gene editing (% indels) as assessed by sequencing for S. pyogenes and S. aureus gRNAs when co-expressed with Cas9 in patient-derived IVS26 primary fibroblasts. FIG. 11B shows gene editing (% indels) as assessed by sequencing for S. aureus gRNAs when co-expressed with Cas9 in HEK293 cells.

Example 4 Detection of gRNA Pair-Induced Deletions by PCR

To assess the ability of a pair of gRNAs to induce a genomic deletion (in which the sequence between the two cut sites is removed), PCR was performed across the predicted deletion. Pairs of gRNAs (encoded as STITCHR products) were co-transfected with pAF003 into IVS26 fibroblasts. Genomic DNA was isolated from transfected cells and PCR was performed to amplify a segment of the CEP290 locus spanning the two predicted cut sites. PCR was run on a QIAxcel capillary electrophoresis machine. The predicted amplicon on a wildtype allele is 1816 bps. Assuming that cleavage occurs within the gRNA target region, amplicon sizes for alleles having undergone the deletion event were calculated and the presence of this smaller band indicates that the desired genomic deletion event has occurred (Table 23).

TABLE 23 Amplicon Deletion Deletion with amplicon Left gRNA Right gRNA Size deletion detected? 1 CEP290-367 CEP290-16 590 1226 no 2 CEP290-367 CEP290-203 688 1128 no 3 CEP290-367 CEP290-132 815 1001 no 4 CEP290-367 CEP290-139 1265 551 no 5 CEP290-312 CEP290-11 790 1026 yes 6 CEP290-312 CEP290-252 973 843 no 7 CEP290-312 CEP290-64 976 840 yes 8 CEP290-312 CEP290-230 1409 407 yes 9 CEP290-12 CEP290-11 19 1797 no 10 CEP290-12 CEP290-252 202 1614 no 11 CEP290-12 CEP290-64 205 1611 no 12 CEP290-12 CEP290-230 638 1178 no 13 CEP290-17 CEP290-16 19 1797 no 14 CEP290-17 CEP290-203 117 1699 no 15 CEP290-17 CEP290-132 244 1572 no 16 CEP290-17 CEP290-139 693 1123 no 17 CEP290-374 CEP290-16 799 1017 no 18 CEP290-374 CEP290-203 897 919 no 19 CEP290-374 CEP290-132 1024 792 no 20 CEP290-374 CEP290-139 1473 343 no 21 CEP290-368 CEP290-16 854 962 no 22 CEP290-368 CEP290-203 952 864 no 23 CEP290-368 CEP290-132 1079 737 no 24 CEP290-368 CEP290-139 1528 288 no 25 CEP290-323 CEP290-11 990 826 yes 26 CEP290-323 CEP290-252 1173 643 no 27 CEP290-323 CEP290-64 1176 640 yes 28 CEP290-323 CEP290-230 1609 207 yes 29 Cas9 only wt amplicon = no 1816 30 GFP only wt amplicon = no 1816 31 no DNA PCR neg ctrl

Example 5 Gene Expression Analysis of CEP290

Targeted deletion of a region containing the IVS26 splice mutation is predicted to correct the splicing defect and restore expression of the normal wild-type CEP290 allele. To quantify expression of the wild-type and mutant (containing additional cryptic splice mutation) alleles, TaqMan assays were designed. Multiple assays were tested for each RNA species and a single wt and single mutant assay were selected. The assay for the wild-type allele contains a forward primer that anneals in exon 26, a reverse primer that anneals in exon 27 and a TaqMan probe that spans the exon26-exon-27 junction. The assay for the mutant allele contains a forward primer that anneals in exon 26, a reverse primer that anneals in the cryptic exon and a TaqMan probe that spans the exon26-cryptic exon junction. A TaqMan assay designed to beta-actin was used as a control. Total RNA was isolated from IVS26 cells transfected with pairs of gRNAs and Cas9-expressing plasmid by either Trizol RNA purification (Ambion), Agencourt RNAdvance (Beckman Coulter) or direct cells-to-Ct lysis (Life Technologies). Reverse transcription to generate cDNA was performed and cDNA was used as a template for qRT-PCR using selected taqman assays on a BioRad real time PCR machine. Relative gene expression was calculated by ΔΔCt, relative to beta-actin control and GFP-only sample. Increases in expression of wt allele and decreases in expression of mutant allele relative to GFP-only control indicate corrected splicing due to gene targeting. FIGS. 12A-12B show initial qRT-PCR data for pairs of gRNAs that had shown activity as either individual gRNAs (measured as described in Example 3) or as pairs (measured as described in Example 4). Pairs of gRNAs that showed the desired gene expression changes were repeated in replicate experiments and the cumulative qRT-PCR data is shown in FIG. 13 (error bars represent standard error of the mean calculated from 2 to 6 biological replicates per sample).

Example 6 Quantification of Genomic Deletions by ddPCR

Droplet digital PCR (ddPCR) is a method for performing digital PCR in which a single PCR reaction is fractionated into 20,000 droplets in a water-oil emulsion and PCR amplification occurs separately in individual droplets. PCR conditions are optimized for a concentration of DNA template such that each droplet contains either one or no template molecules. Assays were designed to perform amplification using BioRad EvaGreen Supermix PCR system with all amplicons ranging in size from 250-350 bp. Control assays were designed to amplify segments of the CEP290 gene at least 5 kb away from the IVS26 c.2991+1655A to G mutation. Assays to detect targeted genomic deletion were designed such that amplification of an allele that has undergone deletion will yield a PCR product in the size range of 250-350 bp and amplification will not occur on a wild-type allele due to the increased distance between forward and reverse primers. PCR conditions were optimized on genomic DNA isolated from 293 cells that had been transfected with pairs of gRNAs and Cas9-expressing plasmid. Deletion assays were verified to generate no positive signal on genomic DNA isolated from unmodified IVS26 fibroblasts. Assays were further tested and optimized on genomic DNA isolated from IVS26 fibroblasts that had been transfected with pairs of gRNAs and Cas9-encoding plasmid. Of the three assays tested for each of two deletions (CEP290-323 and CEP290-11; and CEP290-323 and CEP290-64) and the 4 control assays tested, a single assay was selected for each deletion and a control based on quality data and replicability in the ddPCR assay. FIG. 14 shows deletion rates on three biological replicates calculated by taking the number of positive droplets for the deletion assay and dividing by the number of positive droplets for the control assay.

Example 7 Cloning AAV Expression Vectors

Cloning saCas9 into an AAV Expression Vector

The pAF003 plasmid encodes the CMV-driven S. aureus Cas9 (saCas9), with N-terminal and C-terminal nuclear localization signals (NLS) and a C-terminal triple flag tag, followed by a bovine growth hormone poly(A) tail (bGH polyA). BGH polyA tail was substituted with a 60-bp minimal polyA tail to obtain pAF003-minimal-pA. The CMV-driven NLS-saCas9-NLS-3xFlag with the minimal polyA tail was amplified with PCR and subcloned into pTR-UF11 plasmid (ATCC #MBA-331) with KpnI and Sphl sites to obtain the pSS3 (pTR-CMV-saCas9-minimal-pA) vector. The CMV promoter sequence can be substituted with EFS promoter (pSS10 vector), or tissue-specific promoters (Table 20, e.g. photo-receptor-specific promoters, e.g. Human GRK1, CRX, NRL, RCVRN promoters, etc.) using SpeI and NotI sites.

Constructing the All-in-One AAV Expression Vector with One gRNA Sequence

For each individual gRNA sequence, a STITCHR product with a U6 promoter, gRNA, and the gRNA scaffold was obtained by PCR with an oligonucleotide encoding the gRNA sequence. The STITCHR product with one dsDNA molecule of U6-driven gRNA and scaffold was subcloned into pSS3 or pSS10 vectors using KpnI sites flanking the STITCHR product and downstream of the left Inverted Terminal Repeat (ITR) in the AAV vectors. The orientation of the U6-gRNA-scaffold insertion into pSS3 or pSS10 was determined by Sanger sequencing. Alternate promoters may be used to drive gRNA expression (e.g. H1 promoter, 7SK promoter). Any gRNA scaffold sequences compatible with Cas variants from other bacterial species could be incorporated into STITCHR products and the AAV expression vector therein.

Cloning Two gRNA into an AAV Expression Vector

For each pair of gRNA sequences, two ssDNA oligonucleotides were designed and obtained as the STITCHR primers, i.e. the left STITCHR primer and the right STITCHR primer. Two STITCHR PCR reactions (i.e. the left STITCHR PCR and the right STITCHR PCR) amplified the U6 promoter and the gRNA scaffold with the corresponding STITCHR primer separately. The pSS3 or pSS10 backbone was linearized with KpnI restriction digest. Two dsDNA STITCHR products were purified and subcloned into pSS3 or pSS10 backbone with Gibson Assembly. Due to the unique overlapping sequences upstream and downstream of the STITCHR products, the assembly is unidirectional. The sequences of the constructs were confirmed by Sanger Sequencing. Table 24 lists the names and compositions of AAV expression vectors constructed, including the names of gRNAs targeting human CEP290, the promoter to drive Cas9 expression, and the length of the AAV vector including the Inverted Terminal Repeats (ITRs) from wild type AAV2 genome. Alternative promoters (e.g., H1 promoter or 7SK promoter) or gRNA scaffold sequences compatible with any Cas variants could be adapted into this cloning strategy to obtain the corresponding All-in-One AAV expression vectors with two gRNA sequences.

TABLE 24 Components of AAV expression vectors Length Promoter including Name Left gRNA Right gRNA of saCas9 ITRs pSS10 NA NA EFS 4100 pSS11 CEP290-64 CEP290-323 EFS 4853 pSS15 CEP290-64 NA EFS 4491 pSS17 CEP290-323 NA EFS 4491 pSS30 CEP290-323 CEP290-64 EFS 4862 pSS31 CEP290-323 CEP290-11 EFS 4862 pSS32 CEP290-490 CEP290-502 EFS 4858 pSS33 CEP290-490 CEP290-496 EFS 4858 pSS34 CEP290-490 CEP290-504 EFS 4857 pSS35 CEP290-492 CEP290-502 EFS 4858 pSS36 CEP290-492 CEP290-504 EFS 4857 pSS3 NA NA CMV 4454 pSS8 CEP290-64 CEP290-323 CMV 5207 pSS47 CEP290-323 CEP290-64 CMV 5216 pSS48 CEP290-323 CEP290-11 CMV 5216 pSS49 CEP290-490 CEP290-502 CMV 5212 pSS50 CEP290-490 CEP290-496 CMV 5212 pSS51 CEP290-490 CEP290-504 CMV 5211 pSS52 CEP290-492 CEP290-502 CMV 5212 pSS53 CEP290-492 CEP290-504 CMV 5211 pSS23 NA NA hGRK1 4140 pSS24 NA NA hCRX 3961 pSS25 NA NA hNRL 4129 pSS26 NA NA hRCVRN 4083

Example 8 Assessment of the Functions of All-in-One AAV Expression Vectors

Each individual AAV expression vectors were transfected into 293T cells with TransIT-293 (Mirus, Inc.) to test their function before being packaged into AAV viral vectors. 293T cells were transfected with the same amount of plasmid and harvested at the same time points. SaCas9 protein expression was assessed by western blotting with primary antibody probing for the triple Flag tag at the C-terminus of saCas9, while loading control was demonstrated by αTubulin expression. Deletion events at IVS26 mutation could be determined by PCR amplification followed by Sanger sequencing or ddPCR. The results are shown in FIG. 15.

Example 9 Production, Purification and Titering of Recombinant AAV2 Vectors

Prior to packaging into AAV viral vectors, all AAV expression vector (plasmids) underwent primer walk with Sanger sequencing and function analysis. In recombinant AAV (rAAV), two ITRs flanking the transgene cassettes are the only cis-acting elements from the wild-type AAV. They are critical for packaging intact rAAVs and genome-release for rAAV vectors during transduction. All AAV expression vectors were restriction digested with SmaI or XmaI to ensure the presence of two intact ITRs.

rAAV2 vectors were produced with “Triple Transfection Protocol”: (1) pSS vectors with ITRs and transgene cassettes; (2) pHelper plasmid with E2A, E4, VA genes from Adenovirus; (3) pAAV-RC2 plasmid with Rep and Cap genes from AAV2. These three plasmids were mixed at a mass ratio of 3:6:5 and transfected into HEK293 with polymer or lipid-based transfection reagent (e.g. PEI, PEI max, Lipofectamine, TranslT-293, etc.). 60-72 hours post-transfection, HEK293 cells were harvested and sonicated to release viral vectors. Cell lysates underwent CsCl ultracentrifuge to purify and concentrate the viral vectors. Additional purification procedures were performed to obtain higher purity for biophysical assays, including another round of CsCl ultracentrifuge, or sucrose gradient ultracentrifuge, or affinity chromatography. Viral vectors were dialyzed with 1×DPBS twice before being aliquoted for storage in −80° C. Viral preps can be tittered with Dot-Blot protocol or/and quantitative PCR with probes annealing to sequences on the transgenes. PCR primer sequences are: AACATGCTACGCAGAGAGGGAGTGG (SEQ ID NO: 399) (ITR-Titer-fwd) and CATGAGACAAGGAACCCCTAGTGATGGAG (SEQ ID NO: 400) (ITR-Titer-rev). Reference AAV preps were obtained from the Vector Core at University of North Carolina-Chapel Hill as standards. To confirm the presence of three non-structural viral proteins composing the AAV capsid, viral preps were denatured and probed with anti-AAV VP1/VP2/VP3 monoclonal antibody B1 (American Research Products, Inc. Cat #03-65158) on western blots. The results are shown in FIG. 16.

Example 10 rAAV-Mediated CEP290 Modification In Vitro

293T were transduced with rAAV2 vectors expressing saCas9 with or without gRNA sequences to demonstrate the deletion events near the IVS26 splicing mutant. 293T cells were transduced with rAAV2 viral vectors at an MOI of 1,000 viral genome (vg)/cell or 10,000 vg/cell and harvested at three to seven days post transduction. Western blotting with the primary antibody for Flag (anti-Flag, M2, Sigma-Aldrich) showed that the presence of U6-gRNA-scaffold does not interfere with saCas9 expression. Genomic DNA from 293T was isolated with the Agencourt DNAdvance Kit (Beckman Coulter). Regions including the deletions were PCR amplified from genomic DNA isolated, and analyzed on the QIAxcel capillary electrophoresis machine. Amplicons smaller than the full-length predicted PCR products represent the deletion events in 293T cells. The PCR results are shown in FIG. 17. To further understand the nature of these deletion events, PCR products were cloned into Zero-Blunt TOPO Cloning Kit (Life Technologies) and transformed into chemically competent Top10 cells. Bacterial colonies were then cultured and sequenced using Sanger sequencing. Sequence results were aligned with the wt CEP290 locus for analysis.

Example 11 AAV Transduction of Genome Editing Systems in Mouse Retinal Explants

To assess the ability of the AAV vectors described above to transduce CRISPR/Cas9 genome editing systems into retinal cells in situ, an ex vivo explant system was developed. FIG. 27A shows a representative image of an explanted mouse retina on a support matrix, with the tissue indicated by the gray arrow. Explants were harvested at 7- or 10-day time points, and histological, DNA, RNA and/or protein samples were produced. FIG. 27B shows a representative fluorescence micrograph from a retinal explant treated with an AAV vector carrying a GFP reporter, demonstrating successful transduction of an AAV payload in cells in multiple layers of the retina.

mRNA samples taken from retinal explants further demonstrate that genome editing systems according to the present disclosure are effectively transduced by these AAV vectors: FIG. 28A and FIG. 28B show expression of Cas9 mRNA and gRNA, respectively, normalized to the expression of GAPDH. As expected, untreated samples did not express Cas9 or gRNA, and gRNA was not detected in samples that were not transduced with gRNA coding sequences. Cas9 expression was observed in three AAV constructs in which Cas9 expression was driven by hGRK1, CMV or EFS promoters. The observation of Cas9 mRNA and gRNA in samples transduced with vectors in which Cas9 expression is driven by the retinal photoreceptor cell specific hGRK1 promoter indicates that these vectors can transduce genome editing systems in photoreceptor cells in situ.

DNA samples from retinal explants treated with AAV vectors were sequenced, and indel species were identified. The AAV vectors used in the mouse explant system included guides with targeting domains specific to the mouse CEP290 gene but targeted to the same region of intron 26 as the human guides presented above; aside from the specific guide sequences used, the AAV vectors used were the same as those described above. Table 30 shows a wild type (WT) mouse sequence, with left and right guide sequences italicized, and three representative indels of +1, −4 and −246 aligned with the WT sequence. In the table, three periods ( . . . ) represent an abbreviation of the sequence read for ease of presentation, while dashes (-) represent alignment gaps and underlined nucleotides represent insertions. Insofar as DNA sequencing of explants treated with AAV vectors utilizing the photoreceptor specific hGRK1 promoter revealed indel formation, these data demonstrate genome editing of a CEP290 target site in retinal photoreceptors.

TABLE 30 Representative Indels in Mouse Retinal Explants WT CCCTCAAACACATGTCTCACGCAGCTTAGACATTCT...CAGAACTCGGTCAG-CATGCTACAGATAGCTTATCT         (SEQ ID NO: 2788)                       (SEQ ID NO: 2789) +1 CCCTCAAACACATGTCTCACGCAGCTTAGACATTCT...CAGAACTCGGTCAG G CATGCTACAGATAGCTTATCT         (SEQ ID NO: 2788)                       (SEQ ID NO: 2790) −4 CCCTCAAACACATGTCTCACGCAGCTTAGACATTCT...CAGAACTCGG-----CATGCTACAGATAGCTTATCT         (SEQ ID NO: 2788)                       (SEQ ID NO: 2791) −246 CCCTCAAA G---------------------------...---------------CATGCTACAGATAGCTTATCT         (SEQ ID NO: 2792)                       (SEQ ID NO: 2793)

FIG. 29 summarizes the estimated frequencies of particular editing events in individual mouse explants transduced with AAV vectors according to the present disclosure. In samples transduced with AAV vectors in which Cas9 expression was driven by the hGRK1 promoter, deletions of sequences between gRNAs (guide sites) were consistently observed, as were indels at one of the two guide sites. Indels at one of the two guide sites were also observed in explants transduced with CMV and EFS vectors.

Taken together, these results demonstrate the transduction of CRISPR/Cas9 genome editing systems into cells, including photoreceptor cells, in the intact mouse retina and the editing (including deletion) of a CEP290 target site in retinal photoreceptors in situ.

Example 12 AAV Transduction of Genome Editing Systems in Primate Retina In Vivo

To assess the ability of the AAV vectors described above to transduce CRISPR/Cas9 genome editing systems into retinal cells in vivo, a primate subretinal injection procedure was developed. Cynomolgus macaques received a bilateral subretinal injections of an AAVS vector encoding S. aureus Cas9 operably linked to an EFS, CMV or hGRK promoter sequence, and gRNAs C1 and C2, targeted to an intronic region of the cynomolgus CEP290 gene and comprising targeting sequences as set forth in SEQ ID NOs: 2794 and 2796 respectively (see Table 31). AAV injections were given at dosages of 4×10¹⁰ (low) or 4×10¹¹ (high) viral genomes (vg). Experimental conditions are summarized in Table 32.

TABLE 31 Cynomolgus gRNA Targeting Domain Sequences Targeting Domain Targeting Domain Guide Sequence (DNA) Sequence (RNA) C1 GGCCGGCTAATTTAGTAGAGA GGCCGGCUAAUUUAGUAGAGA (SEQ ID NO: 2794) (SEQ ID NO: 2795) C2 GTTATGAAGAATAATACAAA GUUAUGAAGAAUAAUACAAA (SEQ ID NO: 2796) (SEQ ID NO: 2797)

TABLE 32 Cynomolgus Treatment Conditions Group Vector Dose (vg/eye) CMV-low CEPgRNAs-dCMV-Cas9 4 × 10¹⁰ CMV-high CEPgRNAs-dCMV-Cas9 4 × 10¹¹ EFS-low CEPgRNAs-EFS-Cas9 4 × 10¹⁰ EFS-high CEPgRNAs-EFS-Cas9 4 × 10¹¹ GRK-low CEPgRNAs-GRK1-Cas9 4 × 10¹⁰ GRK-high CEPgRNAs-GRK1-Cas9 4 × 10¹¹ Vehicle GRK1-GFP/Vehicle 4 × 10¹¹

6 or 8 mm retinal tissue punches were obtained from AAV-treated and Vehicle-treated retinas at 6 and 13 weeks post injection, and genomic DNA was harvested. Sequencing was performed by using a proprietary methodology (Uni-Directional Targeted Sequencing, or UDiTaS) described in commonly assigned, copending U.S. Provisional Patent Application No. 62/443,212, which is incorporated by reference herein in its entirety. Data from two UDiTaS sequencing reactions with individual upstream or downstream primers was combined by assuming complete overlap of indels at the two different gRNA cut sites and by averaging the rates of inversions and deletions observed in the two sequencing reactions.

Histological analysis demonstrated successful transduction of primate photoreceptor cells using genome editing systems as disclosed herein. FIG. 27C depicts Cas9 antibody staining in a vehicle-control tissue punch from a primate retina, while FIG. 27D shows Cas9 expression in a punch from a primate retina treated with an AAVS vector encoding S. aureus Cas9 operably linked to an hGRK promoter sequence. The figures show that the outer nuclear layer (ONL) in the AAVS vector-treated punch contains Cas9 protein, while the ONL from the vehicle control punch does not. This demonstrates successful transduction of cells in this layer. No detectable Cas9 expression was detected in cells outside the ONL. Because the hGRK promoter is photoreceptor specific, these data indicate that the systems and methods of this disclosure result in Cas9 expression among retinal photoreceptor cells in primates.

FIG. 30 shows the frequency with which specific edits (indels, insertions, deletions and inversions, were observed in each condition. In both the CMV-high and GRK-high conditions, the frequency of editing events approached or exceeded 40% of reads at the 13-week timepoints. Frequencies of specific edits observed in each experimental condition at each timepoint are listed in Table 33, below. 13 weeks timepoints for the EFS-high condition were not obtained.

TABLE 33 Editing Frequencies Observed in Cynomolgus Treatment Conditions at 6 and 13 Weeks Total Inver- Dele- Inser- editing sions tions tions Indels EFS-low 6 week 2.4% 0.6% 0.4% 0.3% 1.1% 13 week 3.8% 1.2% 0.6% 0.0% 2.0% EFS-high 6 week 10.2% 1.4% 1.3% 2.3% 5.3% 13 week — — — — — CMV-low 6 week 1.1% 0.5% 0.0% 0.1% 0.5% 13 week 13.4% 3.7% 2.1% 0.9% 6.6% CMV-high 6 week 8.0% 0.7% 0.7% 2.1% 4.4% 13 week 44.5% 5.1% 3.7% 11.2% 24.5% GRK-low 6 week 5.0% 0.9% 0.7% 0.7% 2.7% 13 week 1.6% 0.0% 0.0% 0.3% 1.3% GRK-high 6 week 16.6% 2.5% 2.5% 3.5% 8.1% 13 week 38.0% 7.0% 8.5% 5.9% 16.7%

It should be noted that the hGRK1 promoter is photoreceptor specific, and that the genome editing system encoded by the AAV5 vector would only be functional in photoreceptor cells. It is reasonable to conclude, therefore, that the percentages of reads obtained from tissue punches, which include other retinal cell types, are lower than the percentages that would be observed in photoreceptor cells alone. Together, these data demonstrate transduction of a CRISPR/Cas9 system into a primate retina by subretinal injection of AAV, in vivo, and the generation of targeted alterations in a CEP290 gene sequence in primate photoreceptor cells in vivo.

Example 13 Correction of IVS26 Splicing Defect by Inversions and Deletions

To verify that deletions and inversions of the intronic region including the IVS26 mutation correct the splicing defect observed in CEP290 associated disease, a reporter assay was developed utilizing four reporter constructs having the general design depicted in FIG. 31A: pAD26_SplitGFP+WildType_CEP290_Kan (SEQ ID NO: 2798); pAD27_SplitGFP+Mutant_CEP290_Kan (SEQ ID NO: 2799); pAD28_SplitGFP+Mutant_CEP290_Inverted Kan (SEQ ID NO: 2800); and pAD29_SplitGFP+DeletionCEP290_Kan (SEQ ID NO: 2801). These constructs were transfected into U2OS cells at the concentrations shown in FIG. 31B, and GFP and mCherry expression was quantitated for each condition across three bioreplicates. Each of the four reporter constructs included a sequence encoding a split-green-fluorescent protein (GFP) reporter gene incorporating a 2217 bp human CEP 290 intron sequence corresponding to (a) wild type (WT), (b) the IVS26 mutation, (c) a deletion of the intronic sequence between two human CEP290 target sites, including the IVS26 mutation and the cryptic exon observed in mRNAs from subjects with CEP290 associated disease, as would result from the use of a genome editing system according to the present disclosure, or (d) an inversion of the intronic sequence between the two human CEP290 target sites, including the IVS26 mutation and the cryptic exon as would result from the use of a genome editing system of this disclosure. The construct is designed such that correct splicing is necessary for GFP expression. Thus, the presence of the cryptic splice acceptor site in the IVS26 condition, but not the WT condition, will result in disrupted GFP transcripts encoding non-functional GFP proteins; modifications at CEP290 target sites that result in the removal or alteration of the IVS26 mutation would rescue the expression of functional GFP protein. As shown in FIG. 31B, functional GFP protein is expressed at a high baseline level in cells treated with the WT construct, expression is reduced in the IVS26 condition, and is returned to the WT baseline level in the deletion and inversion conditions. These data indicate that the aberrant mRNA splicing caused by the IVS26 mutation is rescued by either deletion or inversion of the intronic sequence comprising that mutation.

Example 14 AAVS Transduction of Genome Editing Systems in Human Retinal Explants

To further establish that the genome editing systems of the present disclosure supported targeted gene editing in human retinal cells, e.g., fully mature human photoreceptors in situ, an ex vivo human retina explant system was developed. Purified AAVS vectors were selected that encoded S. aureus Cas9 operably linked to an hGRK1 or CMV promoter sequence and first and second gRNAs comprising targeting sequences according to SEQ ID NOs: 389 and 388, respectively, and backbone sequences according to SEQ ID NO: 2787. As discussed above, these guides are targeted to the intronic region of the CEP290 gene on opposite sides of the IVS26 A>G mutation (Table 28). Human cadaver donor eyes were obtained within approximately 5 hours post-mortem and 3 mm punches were immobilized on a culture substrate as described above. Retinal explants were treated with AAV vectors at either a low dose of 1×10¹¹ vg or a high dose of 5×10¹¹ vg. Experimental conditions are summarized in Table 34.

TABLE 34 Human Treatment Conditions Group Vector Dose (vg/punch) CMV-low CEPgRNAs-dCMV-Cas9 1 × 10¹¹ CMV-high CEPgRNAs-dCMV-Cas9 5 × 10¹¹ GRK-low CEPgRNAs-GRK1-Cas9 1 × 10¹¹ GRK-high CEPgRNAs-GRK1-Cas9 5 × 10¹¹ Vehicle GRK1-GFP/Vehicle 5 × 10¹¹

DNA samples from human retinal explants treated with AAV vectors were sequenced at either 14 or 28 days post-transduction, and inversions and deletions were identified. FIG. 32 summarizes the productive editing observed in human retinal explants 14 and 28 days after transduction with the various AAV vectors. Productive editing was defined as total edits (equal to the sum of the rates of inversions and deletions) capable of correcting the LCA10-associated splice mutation in the CEP290 gene (FIG. 32). The most productive editing was observed at 16.4% at the 28 day time point for the GRK-high condition. These data demonstrate transduction of a CRISPR/Cas9 system into a human retina by subretinal injection of AAV and the generation of targeted alterations in a CEP290 gene sequence in human photoreceptor cells in situ.

Example 15 AAVS Transduction of Genome Editing Systems in Live Transgenic IVS26 Knock-In Mice

To further establish that the genome editing systems of the present disclosure supported targeted gene editing of the human CEP290 target position in mature photoreceptors in vivo, an IVS26 12 KI mouse model was employed. In this model, the human CEP290 exon 26, intron 26 with the IVS26 mutation (13 c.2991+1655A>G) and exon 27 have been inserted into the murine CEP290 gene via homologous recombination. AAVS vectors encoding (i) S. aureus Cas9 operably linked to the photoreceptor-specific hGRK1 promoter sequence, and (ii) first and second gRNAs comprising targeting sequences according to SEQ ID NOs: 389 and 388, respectively, and having gRNA backbone sequences according to SEQ ID NO: 2787 were used as described in Example 14. The vectors were administered subretinally (toward the temporal side of the retina near the optic nerve) in both eyes of each animal at doses of 1×10¹¹ vg/mL, 1×10¹²vg/mL or 1×10¹³ vg/mL; a vehicle group (containing BSS with 0.014% Tween20) was also used in the study as a control. Subretinal injections were conducted in anesthetized mice in accordance with NIH animal care guidelines. For each injection, a blunt-ended needle (33-gauge, 0.5in; Hamilton company) on a 5m1 Hamilton syringe was inserted through the scleral incision, posterior to the lens, and was advanced centrally toward the temporal retina until resistance was felt. Care was taken to avoid the damaging the lens as the cannula was advanced. A volume of 1 microliter of AAV formulation or vehicle control containing 0.2 mg/mL of fluorescein was injected into the subretinal space, forming a bleb; fluorescein was used to visualize the bleb and to confirm successful injection. Animals were euthanized at 6- and 12-week timepoints, and retinal genomic DNA and RNA were isolated for determining the gene editing efficiency (by UDiTaS) and Cas9/gRNA levels (by RT_PCR), respectively.

Experimental conditions are summarized in Table 35, along with rates of insertion and deletion from individual retinas as measured by UDiTaS.

TABLE 35 Inversion and Deletion Rates in IVS26 KI Mouse Retinas Dose 1 × 10¹² vg 1 × 10¹³ vg Timepoint 6 weeks 12 weeks 6 weeks 12 weeks Inversions 4.68% 3.91% 2.06% 1.88% Deletions 6.29% 5.27% 7.79% 4.13%

These data provide further demonstrate the successful transduction of retinal photoreceptor cells and alteration of the LCA10 target position using the vectors and genome editing systems of the present disclosure.

Example 16 Treatment of Inherited Retinal Dystrophy (e.g., LCA) in Humans Using Recombinant Viral Vectors in Combination with Corticosteroids

The recombinant viral vectors disclosed herein may be used for the treatment of an Inherited Retinal Dystrophy, such as LCA, in a patient in need thereof. In certain embodiments, the patient may have a mutation in the CEP290 gene. For example, the patient may have a mutation in intron 26 (IVS26) of the CEP290 gene (“LCA10-IVS26”). In certain embodiments, the recombinant viral vectors disclosed herein may be used for the treatment of Inherited Retinal Dystrophy with Centrosomal Protein 290 (CEP290)-Related Retinal Degeneration Caused by a Compound Heterozygous or Homozygous Mutation Involving c.2991+1655A>G in Intron 26 (IVS26) of the CEP290 Gene in patient in need thereof. The recombinant viral vector used to treat the patient may be any of the AAV vectors disclosed herein. In certain embodiments, treatment with the AAV vector results in deletion or inversion of the mutation-containing region in the CEP290 gene, leading to improved photoreceptor and visual function. In certain embodiments, the patient may be an adult or pediatric patient.

In certain embodiments, the AAV vector may comprise one or more of the AAV vector genomes as set forth in 19A-F, 20A-20F, 21A-21F, 22A-22F, 23A-23F, 24A-24F. In certain embodiments, the AAV vector may comprise one or more of the AAV vector genomes having the configurations as illustrated in FIGS. 25A-25D. In certain embodiments, the AAV vector may comprise one or more sequences set forth in SEQ ID NOs: 428, 445, 429, 446, 430, 447, 431, 448, 432, 449, 433, 450, 2802, or 2803. The AAV vector may comprise a transgene packaged into AAV serotyped with various AAV capsids, for example, AAV5 capsids. The AAV vector may be formulated in balanced salt solution/0.001% poloxamer 188 (BSSP).

In certain embodiments, the AAV vector may be administered to the patient via sub-retinal injection in the para-foveal region. In certain embodiments, the injection may be a single injection. After completion of a pars plana vitrectomy in the eye to be treated, a subretinal bleb may be formed using the AAV vector as the infusion solution.

In certain embodiments, the patient may be administered an AAV vector at a dose of 9×10¹⁰ viral genomes (vg) to 9×10¹¹ vg (e.g., 9×10¹⁰ vg, 3×10¹¹ vg, or 9×10¹¹ vg)). For example, in certain embodiments, the AAV vector may be administered to the subject at a dose of 3×10¹¹ vg/ml to 3×10¹² vg/ml (e.g., 3×10¹¹ vg/ml, 1×10¹² vg/ml, or 3×10¹² vg/ml). In certain embodiments, the dose may be administered to the patient in a suitable volume (e.g., 0.3 mL).

To mitigate ocular inflammation and associated discomfort, the patient may be administered one or more corticosteroids before, at the same time and/or after administration of the AAV vector. In certain embodiments, the corticosteroid may be an oral corticosteroid (e.g., oral prednisone). In certain embodiments, the patient may be administered the corticosteroid prior to administration of the AAV vector. For example, the patient may be administered the corticosteroid in the days prior to administration of the AAV vector (e.g., 3 days prior to administration of the AAV vector). For example, the corticosteroid treatment may be administered beginning 3 days prior to until 6 weeks after administration of the AAV vector. In certain embodiments, the treatment of corticosteroids may be 0.5 mg/kg/day for 4 weeks, followed by a 15-day taper (0.4 mg/kg/day for 5 days, and then 0.2 mg/kg/day for 5 days, and then 0.1 mg/kg/day for 5 days). The dose of corticosteroid may be changed according to how the patient reacts to the AAV vector. For example, if there is an increase in vitreous inflammation by 1+ on the grading scale while the patient is receiving the 0.5 mg/kg/day dose (i.e., within 4 weeks after surgery), the corticosteroid dose may be may be increased to 1 mg/kg/day. If any inflammation is present within 4 weeks after surgery, the taper may be delayed.

Primary endpoints may include (a) the incidence of dose-limiting toxicity (DLT), such as macular holes, intraocular inflammation, corneal abrasion, corneal edema, decreased visual acuity, vitreous hemorrhage, subretinal hemorrhage, elevated intraocular pressure, eye pain, eye irritation, dry eye, retinal detachment, cataract, endophthalmitis, and ocular infection; (b) number of adverse events related to the AAV vector; and (c) the number of procedural adverse events. Secondary endpoints may include one or more of the following: (a) maximum tolerated dose as determined by DLT, (b) change from baseline in (i) mobility course score, (ii) logMAR measurement of best-corrected visual acuity, (iii) the rate of change, decrease in latency, or absolute change in pupil size following response to light, (iv) dark adapted visual sensitivity, (v) the thickness of the outer nuclear layer, (vi) the Pelli-Robson assessment (vii) macular sensitivity, (viii) Farnsworth 15 score, (ix) retinal function that is measurable by mfERG, (x) age-range specific quality of life instrument and participant Global Impressions of Change and Severity.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned herein are hereby incorporated by reference in their entirety as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

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1-568. (canceled)
 569. A method of altering a cell in an eye of a subject comprising administering to the eye of the subject: an adeno-associated virus (AAV) vector comprising a nucleotide sequence encoding a first guide RNA (gRNA) molecule comprising a first targeting domain complementary with a first target domain from a CEP290 gene and a nucleotide sequence encoding a Cas9 molecule; and a corticosteroid administered daily at a first dose for at least 4 weeks and beginning no more than fourteen days prior to administering the AAV vector.
 570. The method of claim 569, wherein the AAV vector further comprises a nucleotide sequence encoding a second gRNA molecule comprising a second targeting domain complementary with a second target domain from the CEP290 gene.
 571. The method of claim 570, wherein the first targeting domain comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:530 (CEP290-323), SEQ ID NO:555 (CEP290-485), SEQ ID NO:468 (CEP290-490), and SEQ ID NO:538 (CEP290-492).
 572. The method of claim 571, wherein the second targeting domain comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:558 (CEP290-64), SEQ ID NO:2321 (CEP290-11), SEQ ID NO:2312 (CEP290-230), SEQ ID NO:460 (CEP290-496), SEQ ID NO:586 (CEP290-502), and SEQ ID NO:568 (CEP290-504).
 573. The method of claim 572, wherein the corticosteroid is administered at the first dose beginning one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen days prior to administering the AAV vector.
 574. The method of claim 573, wherein the corticosteroid is administered for four weeks, for five weeks, for six weeks, for seven weeks, for eight weeks, for nine weeks, or for ten weeks.
 575. The method of claim 574, wherein the corticosteroid is an oral corticosteroid.
 576. The method of claim 575, wherein the oral corticosteroid is prednisone.
 577. The method of claim 576, wherein the first dose of the corticosteroid is 0.1 mg/kg/per day to 1 mg/kg/day.
 578. The method of claim 577, wherein the first dose of the corticosteroid is 0.5 mg/kg/per day.
 579. The method of claim 577, wherein the first dose of the corticosteroid is 1.0 mg/kg/per day.
 580. The method of claim 578, wherein the AAV vector is administered to the subretinal space of the eye.
 581. The method of claim 580, wherein the corticosteroid is administered at a first dose of at least four weeks and the corticosteroid is then administered at a tapered dose.
 582. A method of altering a cell in an eye of a subject comprising administering to the eye of the subject: a recombinant viral particle comprising a nucleotide sequence encoding a first guide RNA (gRNA) molecule comprising a first targeting domain complementary with a first target domain from a CEP290 gene and a nucleotide sequence encoding a Cas9 molecule; and a corticosteroid administered daily at a first dose for at least 4 weeks and beginning no more than fourteen days prior to administering recombinant viral particle.
 583. The method of claim 582, wherein the recombinant viral particle further comprises a nucleotide sequence encoding a second gRNA molecule comprising a second targeting domain complementary with a second target domain from the CEP290 gene.
 584. The method of claim 583, wherein the first targeting domain comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:530 (CEP290-323), SEQ ID NO:555 (CEP290-485), SEQ ID NO:468 (CEP290-490), and SEQ ID NO:538 (CEP290-492).
 585. The method of claim 584, wherein the second targeting domain comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:558 (CEP290-64), SEQ ID NO:2321 (CEP290-11), SEQ ID NO:2312 (CEP290-230), SEQ ID NO:460 (CEP290-496), SEQ ID NO:586 (CEP290-502), and SEQ ID NO:568 (CEP290-504).
 586. The method of claim 585, wherein the corticosteroid is administered at the first dose beginning one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, or fourteen days prior to administering the recombinant viral particle.
 587. The method of claim 586, wherein the corticosteroid is administered for four weeks, for five weeks, for six weeks, for seven weeks, for eight weeks, for nine weeks, or for ten weeks.
 588. The method of claim 587, wherein the corticosteroid is an oral corticosteroid.
 589. The method of claim 588, wherein the oral corticosteroid is prednisone.
 590. The method of claim 589, wherein the first dose of the corticosteroid is 0.1 mg/kg/per day to 1 mg/kg/day.
 591. The method of claim 590, wherein the first dose of the corticosteroid is 0.5 mg/kg/per day.
 592. The method of claim 590, wherein the first dose of the corticosteroid is 1.0 mg/kg/per day.
 593. The method of claim 591, wherein the AAV vector is administered to the subretinal space of the eye.
 594. The method of claim 593, wherein the corticosteroid is administered at a first dose of at least four weeks and the corticosteroid is then administered at a tapered dose. 